--- /dev/null
+char *PerlScriptName[]={"rec_sum.pl","count.pl","p\
+rocess_list.pl","make_license.pl","CCsed.script","\
+msa2bootstrap.pl","t_coffee_dpa","t_coffee_dpa2","\
+tc_generic_method.pl","generic_method.tc_method","\
+clustalw_method.tc_method","extract_from_pdb","ins\
+tall.pl","clean_cache.pl","nature_protocol.pl","mo\
+cca","dalilite.pl","wublast.pl","blastpgp.pl","ncb\
+iblast_lwp.pl","wublast_lwp.pl","RNAplfold2tclib.p\
+l","fasta_seq2RNAplfold_templatefile.pl","fasta_se\
+q2hmmtop_fasta.pl","fasta_seq2consan_aln.pl","clus\
+talw_aln2fasta_aln.pl","msf_aln2fasta_aln.pl","bla\
+st_aln2fasta_aln.pl","blast_xml2fasta_aln.pl","fas\
+ta_aln2fasta_aln_unique_name.pl","newick2name_list\
+.pl","excel2fasta.pl","any_file2unix_file.pl","End\
+List"};char *PerlScriptFile[]={"use File::Copy;\nu\
+se Env qw(HOST);\nuse Env qw(HOME);\nuse Env qw(US\
+ER);\n$x_field=0;\n$y_field=1;\n$interval=0;\n$fil\
+e=\"stdin\";\n$print_avg=1;\n$print_sd=0;\n$print_\
+sum=0;\n$print_n=0;\nforeach $value ( @ARGV)\n \
+{\n if ($value ne $ARGV[$np]) \n {\n ;\n \
+ }\n elsif($value eq \"-print_all\")\n {\n \
+ $print_sd=$print_avg=$print_n=$print_sum=1;\n \
+ $np++;\n }\n elsif($value eq \"-print_sum\"\
+)\n {\n $print_sum=1;\n $print_avg=0;\\
+n $np++;\n }\n elsif($value eq \"-print_n\\
+")\n {\n $print_n=1;\n $print_avg=0;\n\
+ $np++;\n }\n elsif($value eq \"-print_avg\
+\")\n {\n $print_avg=1;\n $print_avg=0\
+;\n $np++;\n }\n elsif($value eq \"-sd\")\\
+n {\n $print_sd=1;\n $print_avg=0;\n \
+ $np++;\n }\n elsif($value eq \"-h\")\n \
+{\n $header=1;\n $np++;\n }\n elsif ($\
+value eq \"-i\")\n {\n $interval= $ARGV[++\
+$np];\n $np++;\n }\n elsif ($value eq \
+\"-r\")\n {\n $min= $ARGV[++$np];\n $m\
+ax= $ARGV[++$np];\n $np++;\n }\n \n el\
+sif ($value eq \"-x\")\n {\n $x_field= $AR\
+GV[++$np]-1;\n $np++;\n }\n elsif ($va\
+lue eq \"-y\")\n {\n \n while ($ARGV\
+[$np+1] && !($ARGV[$np+1]=~/\\-/))\n {\n $y\
+_field[$nyf++]=$ARGV[++$np]-1;\n $y_field_set=1;\\
+n }\n\n $np++;\n }\n elsif ($val\
+ue eq \"-file\")\n {\n $file= $ARGV[++$np]\
+;\n $file_set=1;\n $np++;\n } \
+ \n elsif ( $value eq \"h\" || $value eq \"-h\" \
+|| $value eq \"-H\" || $value eq \"-help\" || $val\
+ue eq \"help\")\n {\n print STDOUT \"data_an\
+alyse: Analyse and discretization of data\\n\";\n \
+ print STDOUT \" -file: <file containi\
+ng the data to analyze>,.<def=STDIN>\\n\";\n p\
+rint STDOUT \" -x: <field containing the X>,\
+...............<Def=0>\\n\";\n print STDOUT \"\
+ -y: <field containing the Y>,..............\
+.<Def=1>\\n\";\n print STDOUT \" -i:<Int\
+erval size on the X>,...............<Def=0>\\n\";\\
+n print STDOUT \" -i:<0:only one interva\
+l>\\n\";\n print STDOUT \" -r:<Range of \
+the X>\\n\";\n print STDOUT \" -sd: prin\
+t standard deviation on the Y\";\n print STDOU\
+T \" -h : print column header \\n\";\n \
+exit (0);\n }\n elsif ($value=~/-/)\n {\n \
+print \"$value is not a valid FLAG[FATAL]\\n\";\n \
+ exit (0);\n } \n elsif ($list eq \"\") \n \
+ {\n $file=$ARGV[$np];\n $np++;\n }\\
+n \n \n }\n\n\n\n\n\nif ($file eq \"stdin\")\\
+n {\n $remove_file=1;\n $file=\"tmp$$\";\n open (F\
+, \">$file\");\n while (<STDIN>)\n {\n print F $\
+_;\n }\n close (F);\n \n ;}\n\n\nopen(F,$file);\\
+n\nif ($interval)\n {\n $interval_size=($max-$\
+min)/$interval;\n }\nwhile (<F>)\n {\n $line=\
+$_;\n if (!/\\S/){next;}\n @list=($line=~/(\\
+\S+)/g);\n \n if ($interval==0){$bin=0;}\n \
+ else{$bin=int (($list[$x_field]-$min)/($interval\
+_size));}\n\n \n if ($bin && $bin==$interval\
+){$bin--;}\n for ( $a=0; $a<$nyf; $a++)\n \
+{\n $sum{$a}{$bin}+=$list[$y_field[$a]];\n $sum2{$\
+a}{$bin}+=$list[$y_field[$a]]*$list[$y_field[$a]];\
+\n $n{$a}{$bin}++;\n }\n }\n\nif (!$interval\
+){$interval=1;}\nfor ( $a=0; $a<$interval; $a++)\n\
+ {\n printf ( \"%3d %3d \", $interval_size*$a,\
+ $interval_size*($a+1));\n for ( $b=0; $b<$nyf;\
+ $b++) \n {\n $i=$interval*$a;\n if ( $n{$b}{\
+$a}==0)\n {\n $avg=0;\n $sd=0;\n }\n e\
+lse\n {\n $avg=$sum{$b}{$a}/$n{$b}{$a};\n \
+ $sd=sqrt($sum2{$b}{$a}*$n{$b}{$a}-$sum{$b}{$a}*$\
+sum{$b}{$a})/($n{$b}{$a}*$n{$b}{$a});\n }\n if (\
+$print_n) {printf \"%10.4f \", $n{$b}{$a};}\n if (\
+$print_sum){printf \"%10.4f \", $sum{$b}{$a};}\n i\
+f ($print_avg){printf \"%10.4f \", $avg}\n if ($pr\
+int_sd) {printf \"%10.4f \", $sd;}\n }\n p\
+rintf (\"\\n\");\n }\n\n\nif ( $remove_file){unli\
+nk $file;}\n","use File::Copy;\nuse Env qw(HOST);\\
+nuse Env qw(HOME);\nuse Env qw(USER);\n\nforeach $\
+v (@ARGV){$cl.=$v;}\n\n\nif ( $cl=~/-k(\\d+)/){$k=\
+$1;}\nelse {$k=1;}\nif ( $cl=~/-w(\\d+)/){$w=$1;}\\
+nelse {$w=-1;}\nif ( $cl=~/-p(\\d+)/){$p=$1;}\nels\
+e {$p=-1;}\n\nwhile (<STDIN>)\n {\n @l=($_=~/(\
+\\S+)/g);\n $v=$l[$k-1];\n if ( !$h{$v}){@ll\
+=($v, @ll);}\n \n if ( $w==-1)\n {$h{$v\
+}++;}\n else\n {$h{$v}+=$l[$w-1];}\n\n \
+if ($p!=-1){$print{$v}=$l[$p-1];}\n\n }\nforeach \
+$v (@ll)\n {\n print \"$v $print{$v} $h{$v}\\n\
+\";\n }\n","\nuse Env qw(HOST);\nuse Env qw(HOME)\
+;\nuse Env qw(USER);\n$random_tag=int (rand 10000)\
++1;\n$unique_prefix=\"$$.$HOST.$random_tag\";\n$qu\
+eue=\"distillery.and.mid\";\n$monitor=0;\n$stderr_\
+file=\"/dev/null\";\n$stdio_file=\"/dev/null\";\n$\
+log_file=\"/dev/null\";\n$pause_time=0;\n$max_sub_\
+jobs=60;\n$min_sub_jobs=30;\n$output_all=0;\n$var=\
+'\\$';\n\nforeach $value ( @ARGV)\n {\n if ($va\
+lue ne $ARGV[$np]) \n {\n ;\n }\n elsi\
+f ($value eq \"-max_sub_jobs\")\n {\n $max\
+_sub_jobs= $ARGV[++$np];\n $np++;\n } \
+\n elsif ($value eq \"-min_sub_jobs\" )\n {\n \
+ $min_sub_jobs= $ARGV[++$np];\n $np++;\n \
+ }\n elsif ($value eq \"-para\")\n {\n \
+ $para=1;\n $monitor=1;\n $np++;\n \
+ }\n elsif ($value eq \"-monitor\") \n {\n \
+ $monitor=1;\n $np++;\n }\n elsif ($value\
+ eq \"-no_monitor\") \n {\n $monitor=0;\n \
+ $np++;\n }\n elsif ($value eq \"-queue\")\\
+n {\n $queue=$ARGV[++$np];\n $np++;\n \
+ } \n elsif ($value eq \"-stderr_file\")\n \
+{\n $stderr_file=$ARGV[++$np];\n $np++;\n \
+ }\n elsif ($value eq \"-stdio_file\")\n {\\
+n $stdio_file=$ARGV[++$np];\n $np++;\n \
+ }\n elsif ($value eq \"-output_all\")\n {\n \
+ $output_all=1;\n $np++;\n }\n elsif ($v\
+alue eq \"-pause\") \n {\n $pause_time=$AR\
+GV[++$np];\n $np++;\n }\n elsif ($value eq\
+ \"-log\")\n {\n $log=1;\n \n \
+ if ($ARGV[$np+1]=~/\\-\\S+/) \n {\
+\n $log_file=\"stderr\";\n }\n \
+ else \n {\n $log_file=$ARGV[++$np]; \
+\n ++$np;\n \n }\n }\n elsif \
+( $value eq \"-com\")\n {\n \n if (!$ARGV[$n\
+p+1]=~/^\\'/) { $com=$ARGV[++$np];}\n else {$com=\
+$ARGV[++$np];}\n\n $np++;\n }\n elsif ( $\
+value eq \"-check\")\n {\n \n if (!$ARGV\
+[$np+1]=~/^\\'/) { $check=$ARGV[++$np];}\n els\
+e {$check=$ARGV[++$np];}\n $np++;\n }\n elsi\
+f ($com eq \"\") \n {\n $com_set=1;\n \
+$com=$ARGV[$np];\n \n $np++;\n }\n els\
+if ($list eq \"\") \n {\n $list_set=1;\n \
+ $list=$ARGV[$np];\n $np++;\n }\n elsif \
+( $var_set eq \"\")\n {\n $var_set=1;\n \
+ $var=$ARGV[$np];\n $np++;\n }\n }\n\n\n\\
+n\nif ( $com eq \"\"){print \"You Need to Provide \
+a Command [FATAL]\\n\";\n die;\n }\n\n\\
+n\nif ($list_set==0) \n {\n $x= int (rand 10\
+0000)+1;\n $tmp_file_name=\"tmp_file_$x\";\n \
+ open ( TMP, \">$tmp_file_name\");\n while (<ST\
+DIN>)\n {\n print TMP $_;\n }\n close\
+ (TMP);\n open (F, $tmp_file_name);\n }\nels\
+e \n {\n open (F, $list);\n }\n\nif ($par\
+a==0) \n {\n\n @tc_list= <F>;\n close (\
+F); \n \n foreach $val(@tc_list) \n {\\
+n \n \n \n $loc_com=$com;\\
+n if ($check){$loc_check=$check;}\n \n\
+ @i_val=($val=~/([^\\s]+)/g);\n \n \
+ if ( $#i_val==0)\n {\n if ($check){$loc_che\
+ck=~s/$var/$i_val[0]/g;}\n $loc_com=~s/$var/$i_\
+val[0]/g;\n }\n else\n {\n for ($n=1; $\
+n<=$#i_val+1;$n++ )\n {\n \n $s\
+ub=\"$var$n\";\n \n $loc_com=~s/$sub\
+/$i_val[$n-1]/g;\n if ($check){$loc_check=~\
+s/$var/$i_val[0]/g;}\n }\n }\n if ( $c\
+heck && -e $loc_check)\n {\n print STDERR \"sk\
+ipping $loc_com...\\n\";\n }\n else\n {\\
+n system \"$loc_com\";\n }\n }\n exit;\\
+n }\n\nelsif ($para==1) \n {\n print STDE\
+RR \"do parallel execution of: \\\"$com $list\\\"\\
+\n\";\n \n if ($log==1) \n {\n if ($log_file\
+ eq \"stdout\" || $log_file eq \"stderr\" ) \n {\\
+n $log_file=\"\";\n }\n\n else \n \
+ {\n system \"echo LOG FILE> $log_file\";\n \n \
+ }\n }\n else \n {\n open ( OUT, \">/dev/\
+null\");\n }\n \n \n $id=0;\n $n_sub=0;\n\
+ while ($val=<F>) \n { \n $job\
+_log[$id]=\"$HOME/tmp/$unique_prefix.$id.log_file\\
+";\n \n $job=$unique_prefix.\"_$id\";\n \
+ open (JOB, \">$job\");\n \n $loc_com=$co\
+m;\n chop $val;\n\n $loc_com=~s/\\$/$val/g\
+;\n \n print JOB \"#!/bin/csh\\n\";\n pri\
+nt JOB \"#\\$ -cwd\\n\";\n print JOB \"#\\$ -N\
+ $unique_prefix\\n\";\n if ($queue && !($queue\
+ eq \" \")) {print JOB \"#\\$ -l $queue\\n\";}\n \
+ print JOB \"#\\n\"; \n print JOB\
+ \"$loc_com\\n\";\n print JOB \"echo FINISHED \
+ >> $job_log[$id]\\n\";\n print JOB \"pwd\\n\"\
+;\n \n close (JOB);\n if ( $output_all\
+==1)\n {\n system \"qsub $job > $unique_prefix\\
+"; \n }\n else\n {system \"qsub $job\
+ -e $stderr_file -o $stdio_file >$unique_prefix\";\
+ \n } \n\n\n\n print STDERR \"\
+$id: $output_all\\n\";\n $n_sub++;\n if ( \
+$max_sub_jobs && $n_sub==$max_sub_jobs) \n {\n $\
+n_sub=monitor_process($min_sub_jobs,@job_log); \
+\n \n } \n \n unlink $uniqu\
+e_prefix;\n sleep $pause_time;\n $id++;\n \
+ }\n\n close (OUT);\n close (F);\n\n p\
+rint STDERR \"Your $id Jobs Have Been Submited (NA\
+ME=$unique_prefix)\\n\";\n monitor_process (0, \
+@job_log);\n foreach $file(@job_log) {if (-e $f\
+ile) {unlink($file);}}\n \n }\n\nsub monitor\
+_process ( @job_list)\n {\n my (@job_list)=@\
+_;\n my $min_sub_jobs=shift (@job_list);\n m\
+y $n_sub_jobs;\n my $finished;\n my $n=0;\n\\
+n $n_sub_jobs=-1;\n $finished=0;\n print \
+STDERR \"\\nMonitor Batch: [$min_sub_jobs]\";\n \
+ \n while (!$finished && (($n_sub_jobs>$min_\
+sub_jobs)|| $n_sub_jobs==-1) ) \n {\n $finished=1;\
+\n $n_sub_jobs=0;\n $n=0;\n foreach $file (@job_li\
+st)\n {\n \n if (-e $file){;}\n else \n \
+ {\n $finished=0; $n_sub_jobs++;\n \
+ }\n }\n system \"sleep 1\";\n \
+ }\n \n return $n_sub_jobs;\n }\n \n \
+ \nif ($tmp_file_name){unlink($tmp_file_name);}\n\
+","\n\nforeach ($np=0; $np<=$#ARGV; $np++)\n {\\
+n $value=$ARGV[$np];\n\n if ($value eq \"-fi\
+le\")\n {\n $file= $ARGV[++$np];\n \
+}\n elsif ($value eq \"-type\")\n {\n \
+ $type= $ARGV[++$np];\n }\n elsif ($valu\
+e eq \"-institute\")\n {\n $institute=\
+ $ARGV[++$np];\n }\n elsif ($value eq \"-a\
+uthor\")\n {\n $author= $ARGV[++$np];\\
+n }\n elsif ($value eq \"-date\")\n {\
+\n $date= $ARGV[++$np];\n }\n elsi\
+f ($value eq \"-program\")\n {\n $prog\
+ram= $ARGV[++$np];\n }\n elsif ($value eq \
+\"-email\")\n {\n $email= $ARGV[++$np]\
+;\n }\n else\n {\n print \"$value is \
+an unkown argument[FATAL]\\n\";\n exit (1);\n \
+ }\n }\n\n\n\nopen F, $file || die;\nprint $INSTI\
+TUTE;\nif ( $type eq \"c\"){print \"/*************\
+*****************COPYRIGHT NOTICE*****************\
+**************/\\n\";}\nif ( $type eq \"perl\"){pr\
+int \"##############################COPYRIGHT NOTI\
+CE##############################/\\n\";}\nif ( $ty\
+pe eq \"txt\"){print \"---------------------------\
+----COPYRIGHT NOTICE------------------------------\
+/\\n\";}\n\n\nwhile (<F>)\n {\n s/\\$INSTITUTE/$\
+institute/g;\n s/\\$AUTHOR/$author/g;\n s/\\$DAT\
+E/$date/g;\n s/\\$PROGRAM/$program/g; \n s/\\$E\
+MAIL/$email/g; \n if ( $type eq \"txt\"){print $\
+_;}\n elsif ($type eq \"c\"){chop $_; print \"\\/\
+*$_*\\/\\n\";}\n elsif ($type eq \"perl\"){print \
+\"\\#$_\";}\n}\nclose (F);\nif ( $type eq \"c\"){p\
+rint \"/******************************COPYRIGHT NO\
+TICE*******************************/\\n\";}\nif ( \
+$type eq \"perl\"){print \"#######################\
+#######COPYRIGHT NOTICE###########################\
+###/\\n\";}\nif ( $type eq \"txt\"){print \"------\
+-------------------------COPYRIGHT NOTICE---------\
+---------------------/\\n\";}\n\n","\nwhile (<>) \\
+n {\n s/\\=cc/123456789/g;\n s/\\bcc/\\$\\(CC\\)/g\
+;\n s/123456789/\\=cc/g;\n print $_;\n }\n\n","$ve\
+rsion=\"1.00\";\n$rseed= int(rand(100000))+1;\n\n\\
+nif ( $#ARGV==-1)\n {\n print \"msa2bootstrap \
+-i <input_file> -input <seq|msa|matrix|tree> -n <N\
+-Boostrap> -o <outtree> -tmode <nj|upgma|parsimony\
+|ml> -dmode <kimura> -alignpg <t_coffee | muscle |\
+ clustalw> -rtree <file> -stype <prot|cdna|dna> -r\
+ecompute -system <cygwin|unix>\";\n print \"\\n\
+\\t-i: input file, can be sequneces, msa, matrix, \
+trees, type is specified via -input\";\n print \
+\"\\n\\t-input: Type of input data\";\n print \\
+"\\n\\t\\tmsa: msa in fasta format\";\n print \\
+"\\n\\t\\tseq: compute an msa with -alignpg\";\n \
+ print \"\\n\\t\\tmatrix: phylipp distance matrix\
+ fed directly to method -tmode [caveat: tmode=nj o\
+r upgma]\";\n print \"\\n\\t\\ttree: list of ne\
+wick trees directly fed to consence in order to ge\
+nerate a bootstraped tree\";\n \n print \"\\\
+n\\t-n: number of bootstrap replicates\";\n pri\
+nt \"\\n\\t-o: name of the output tree. Files are \
+not overwritten. Use -recompute to overwrite exist\
+ing file\";\n print \"\\n\\t-tmode: tree mode: \
+nj|upgma|parsimony|ml\";\n print \"\\n\\t-dmode\
+: distance mode\";\n print \"\\n\\t-alignpg: pr\
+ogram for aligning sequences (t_coffee=default)\";\
+\n print \"\\n\\t-rtree: replicate tree file (d\
+efault: no file)\";\n print \"\\n\\t-rmsa: repl\
+icate msa file (default: no file)\";\n print \"\
+\\n\\t-rmat: replicate matrix file (default: no fi\
+le)\";\n print \"\\n\\t-stype: sequence type: p\
+rotein, dna or cdna\";\n print \"\\n\\t-recompu\
+te: force files to be overwritten\";\n print \"\
+\\n\\t-system: cygwin|unix\";\n \n\n \n \
+ &my_exit (EXIT_FAILURE);\n }\nforeach $arg (@ARG\
+V){$command.=\"$arg \";}\n\nprint \"CLINE: $comman\
+d\\n\";\n$threshold=100;\n$trim_msa=0;\n$stype=\"p\
+rot\";\nprint \"msa2bootstrap \";\n\n$system=\"cyg\
+win\";\nif(($command=~/\\-system (\\S+)/))\n {\n \
+ $system=$1;\n if ( $system eq \"cygwin\")\n \
+ {\n $exec_extension=\".exe\";\n }\n e\
+lsif ( $system eq \"unix\")\n {\n $exec_exten\
+sion=\"\";\n print \"system=Unix\";die;\n }\n\
+ else\n {\n print \"msa2boostrap: -system=\
+$system is an unknown mode [FATAL]\\n\"; die;\n \
+ }\n \n print \"-system $system \";\n }\n\
+if(($command=~/\\-stype (\\S+)/))\n {\n $stype\
+=$1;\n }\nprint \"-stype=$stype \";\n\n\n\nif(($c\
+ommand=~/\\-i (\\S+)/))\n {\n $msa=$1;\n pr\
+int \"-i $msa \";\n }\n\nif(($command=~/\\-rtree \
+(\\S+)/))\n {\n $rtree=$1;\n print \"-rtree\
+=$rtree \";\n }\n\nif(($command=~/\\-rmsa (\\S+)/\
+))\n {\n $rmsa=$1;\n }\nif(($command=~/\\-rma\
+t (\\S+)/))\n {\n $rmat=$1;\n }\n$input=\"seq\
+\";\nif(($command=~/\\-input (\\S+)/))\n {\n $\
+input=$1;\n }\nprint \"-input=$input \";\n\n$dmod\
+e=\"kimura\";\nif(($command=~/\\-dmode (\\S+)/))\n\
+ {\n $dmode=$1;\n }\nprint \"-dmode=$dmode \"\
+;\n$alignpg=\"muscle\";\nif(($command=~/\\-alignpg\
+ (\\S+)/))\n {\n $alignpg=$1;\n }\nprint \"-a\
+lignpg=$dmode \";\n\n$tmode=\"nj\";\nif(($command=\
+~/\\-tmode (\\S+)/))\n {\n $tmode=$1;\n }\npr\
+int \"-tmode=$tmode \";\n$recompute=0;\nif(($comma\
+nd=~/\\-recompute/))\n {\n $recompute=1;\n \
+print \"-recompute \";\n }\n\n$out=$msa;\n$out=~s\
+/\\..*//;\n$out.=\".bph\";\nif(($command=~/\\-o (\\
+\S+)/))\n {\n $out=$1;\n \n }\nprint \"-ou\
+t=$out \";\nif (-e $out && !$recompute)\n {\n \
+print \"\\nNo Computation Required $out already ex\
+ists\\n\";\n &my_exit (EXIT_SUCCESS);\n \n \
+}\n\n$n=100;\nif(($command=~/\\-n (\\d+)/))\n {\n\
+ $n=$1;\n }\nprint \"-n=$n \";\n$seed=3;\nif((\
+$command=~/\\-s (\\d+)/))\n {\n $seed=$1;\n }\
+\nprint \"-s=$seed \";\n\nif(($command=~/\\-run_na\
+me (\\d+)/))\n {\n $suffix=$1;\n }\nelse\n {\
+\n $msa=~/([^.]+)/;\n $suffix=$1;\n }\nprin\
+t \"-run_name=$suffix\\n\";\n\n\nif ( $input eq \"\
+seq\")\n {\n $seq=$msa;\n $msa=\"$suffix.pr\
+ot_msa\";\n \n if ($stype eq \"cdna\")\n \
+ {\n $cdna_seq=$seq;\n $clean_cdna_seq=&vtmpnam()\
+;\n $seq=&vtmpnam();\n `t_coffee -other_pg seq_ref\
+ormat -in $cdna_seq -action +clean_cdna >$clean_cd\
+na_seq`;\n `t_coffee -other_pg seq_reformat -in $c\
+lean_cdna_seq -action +translate >$seq`;\n \n \
+ }\n\n if (!-e $msa || $recompute)\n {\n p\
+rint \"\\n##### Compute an MSA With $alignpg\\n\\
+";\n \n if ( $alignpg eq \"t_coffee\")\n {`$alig\
+npg $seq -outfile=$msa >/dev/null 2>/dev/null`;}\n\
+ elsif ( $alignpg eq \"muscle\")\n {\n `$ali\
+gnpg -in $seq > $msa 2>/dev/null`;\n }\n elsif (\
+ $alignpg eq \"clustalw\")\n {\n `$alignpg -\
+infile=$seq -outfile=$msa -quicktree >/dev/null 2>\
+/dev/null`;\n }\n elsif ( $align eq \"mafft\")\n\
+ {\n `$alignpg $seq > $msa >/dev/null 2>/dev\
+/null`;\n }\n else\n {\n `$alignpg -in=$se\
+q -outfile=$msa`;\n }\n }\n if (!-e $msa\
+)\n {\n print \"\\nError: $alignpg Could Not \
+produce the MSA $msa [FATAL]\\n\";\n }\n\n \
+ if ($stype eq \"cdna\")\n {\n $msa2=\"$suffi\
+x.cdna_msa\";\n `t_coffee -other_pg seq_reformat -\
+in $clean_cdna_seq -in2 $msa -action +thread_dna_o\
+n_prot_aln -output fasta_aln >$msa2`;\n $msa=$msa\
+2;\n }\n \n $input=\"msa\";\n }\n\n\n\\
+n$seqboot_o=&vtmpnam();\n$seqboot_c=&vtmpnam();\n\\
+n$protdist_o=&vtmpnam();\n$protdist_c=&vtmpnam();\\
+nif ( $input eq \"msa\")\n {\n if ($tmode eq \\
+"nj\" || $tmode eq \"upgma\"){$input=\"matrix\";}\\
+n \n $lmsa= &vtmpnam ();\n `t_coffee -oth\
+er_pg seq_reformat -in $msa -output phylip_aln > $\
+lmsa`;\n \n if ( -e \"outfile\"){unlink (\"o\
+utfile\");}\n # run seqboot\n \n if ( $n>1)\
+\n {\n print \"Run SeqBoot .....\";\n open (F\
+, \">$seqboot_c\");\n print F \"$lmsa\\nR\\n$n\\nY\
+\\n$seed\\n\";\n close (F);\n `seqboot$exec_extens\
+ion < $seqboot_c`;\n if ( -e \"outfile\"){ print \
+\"[OK]\\n\";}\n else { print \"[FAILED]\\n\";&my_e\
+xit (EXIT_FAILURE);}\n `mv outfile $seqboot_o`;\n \
+ }\n else\n {\n `cp $lmsa $seqboot_o`;\
+\n }\n\n if ($rmsa){`cp $seqboot_o $rmsa`;\
+}\n \n if ($tmode eq \"nj\" || $tmode eq \"u\
+pgma\")\n {\n if ( $stype eq \"prot\")\n {\\
+n # run protdist\n print \"Run Protdist [d\
+mode=$dmode]\";\n if ($dmode eq \"kimura\")\n \
+ {\n $dmode=\"P\\nP\\nP\";\n }\n e\
+lse\n {\n print \"\\n$dmode is an unknown m\
+ode for Protdist [FATAL:msa2bootstrap.pl]\\n\";\n \
+ &my_exit (EXIT_FAILURE);\n }\n open (F,\
+ \">$protdist_c\");\n if ($n>1){print F \"$seq\
+boot_o\\n$dmode\\nM\\nD\\n$n\\nY\\n\";}\n else\
+ {printf F \"$seqboot_o\\n$dmode\\nY\\n\";}\n \
+close (F);\n `protdist$exec_extension < $prot\
+dist_c`;\n if ( -e \"outfile\"){ print \"[OK]\\
+\n\";}\n else { print \"[FAILED]\\n\";&my_exit\
+ (EXIT_FAILURE);}\n `mv outfile $protdist_o`;\\
+n \n }\n elsif ( $stype eq \"cdna\" || $stype e\
+q \"dna\")\n {\n print \"Run dnadist [dmode=\
+default\";\n open (F, \">$protdist_c\");\n \
+ if ($n>1){print F \"$seqboot_o\\nM\\nD\\n$n\\nY\\\
+n\";}\n else {printf F \"$seqboot_o\\nY\\n\";}\
+\n close (F);\n `protdist$exec_extension \
+< $protdist_c`;\n if ( -e \"outfile\"){ print \
+\"[OK]\\n\";}\n else { print \"[FAILED]\\n\";&\
+my_exit (EXIT_FAILURE);}\n `mv outfile $protdi\
+st_o`;\n }\n }\n }\nelsif ( $input eq \"ma\
+trix\")\n {\n $protdist_o=&vtmpnam();\n pri\
+nt \"MSA: $msa\\n\";\n `cp $msa $protdist_o`;\n\
+ $n=1;\n }\n\n\n\n\n\n$nb_o=&vtmpnam();\n$nb_c\
+=&vtmpnam();\nif ($input eq \"matrix\" && $tmode n\
+e \"parsimony\" && $tmode ne \"ml\")\n {\n pri\
+nt \"Run neighbor [tmode=$tmode]\";\n\n if ($tm\
+ode eq \"nj\")\n {\n $tmode=\"\\nN\\nN\";\n \
+ }\n elsif ( $tmode eq \"upgma\")\n {\n\
+ $tmode = \"\\nN\";\n }\n else\n {\n \
+print \"\\n ERROR: $tmode is an unknown tree compu\
+tation mode\\n\";\n &my_exit (EXIT_FAILURE);\n \
+ }\n\n open (F, \">$nb_c\");\n if ($n>1){pr\
+int F \"$protdist_o$tmode\\nM\\n$n\\n$seed\\nY\\n\\
+";}\n else {print F \"$protdist_o$tmode\\nY\\n\\
+";}\n close (F);\n\n `neighbor$exec_extensio\
+n < $nb_c`;\n if ( -e \"outtree\"){ print \"[N\
+eighbor OK]\\n\";}\n else { print \"[FAILED]\\n\
+\";&my_exit (EXIT_FAILURE);}\n `mv outtree $nb_\
+o`;\n unlink (\"outfile\");\n }\nelsif ($input\
+ eq \"msa\" && $tmode eq \"parsimony\")\n {\n \
+if ( -e \"outfile\"){unlink (\"outfile\");}\n i\
+f ( -e \"outtree\"){unlink (\"outtree\");}\n \n\
+ if ($stype eq \"prot\")\n {\n print \"Run\
+ protpars [tmode=$tmode]\";\n open (F, \">$nb_c\")\
+;\n if ($n>1){print F \"$seqboot_o\\nM\\nD\\n$n\\n\
+$seed\\n10\\nY\\n\";}\n else {print F \"$seqboot_o\
+\\nY\\n\";}\n close (F);\n `protpars$exec_extensio\
+n < $nb_c`;\n }\n elsif ( $stype eq \"dna\
+\" || $stype eq \"cdna\")\n {\n print \"Run d\
+napars [tmode=$tmode]\";\n open (F, \">$nb_c\");\n\
+ if ($n>1){print F \"$seqboot_o\\nM\\nD\\n$n\\n$se\
+ed\\n10\\nY\\n\";}\n else {print F \"$seqboot_o\\n\
+Y\\n\";}\n close (F);\n `dnapars$exec_extension <\
+ $nb_c`;\n }\n if ( -e \"outtree\"){ print\
+ \"[OK]\\n\";}\n else { print \"[FAILED]\\n\";&\
+my_exit (EXIT_FAILURE);}\n `mv outtree $nb_o`;\\
+n unlink (\"outfile\");\n }\nelsif ($input eq \\
+"msa\" && $tmode eq \"ml\")\n {\n if ( -e \"ou\
+tfile\"){unlink (\"outfile\");}\n if ( -e \"out\
+tree\"){unlink (\"outtree\");}\n \n if ($sty\
+pe eq \"prot\")\n {\n print \"Error: ML impos\
+sible with Protein Sequences [ERROR]\";\n &my_exit\
+ (EXIT_FAILURE);\n }\n elsif ( $stype eq \\
+"dna\" || $stype eq \"cdna\")\n {\n print \"R\
+un dnaml [tmode=$tmode]\";\n open (F, \">$nb_c\");\
+\n if ($n>1){print F \"$seqboot_o\\nM\\nD\\n$n\\n$\
+seed\\n10\\nY\\n\";}\n else {print F \"$seqboot_o\\
+\nY\\n\";}\n close (F);\n `dnaml$exec_extension <\
+ $nb_c`;\n }\n if ( -e \"outtree\"){ print\
+ \"[OK]\\n\";}\n else { print \"[FAILED]\\n\";&\
+my_exit (EXIT_FAILURE);}\n `mv outtree $nb_o`;\\
+n unlink (\"outfile\");\n }\n\n\nelse\n {\n \
+ `cp $msa $nb_o`;\n $n=2;\n }\n\nif ($rmsa && \
+-e $seqboot_o){print \"\\nOutput List of $n Replic\
+ate MSA: $rmsa\\n\";`cp $seqboot_o $rmsa`;}\nif ($\
+rmat && -e $protdist_o){print \"\\nOutput List of \
+$n Replicate MATRICES: $rmat\\n\";`cp $protdist_o \
+$rmat`;}\nif ($rtree && -e $nb_o){print \"\\nOutpu\
+t List of $n Replicate TREES: $rtree\\n\";`cp $nb_\
+o $rtree`;}\n\n\n\n$con_o=&vtmpnam();\n$con_c=&vtm\
+pnam();\nif ($n >1)\n {\n print \"Run Consense\
+.....\";\n open (F, \">$con_c\");\n print F \
+\"$nb_o\\nY\\n\";\n close (F);\n `consense$e\
+xec_extension < $con_c`;\n if ( -s \"outtree\"\
+ > 0) { print \"[OK]\\n\";}\n else { print \"[\
+FAILED]\\n\";&my_exit (EXIT_FAILURE);}\n `mv ou\
+ttree $con_o`;\n unlink (\"outfile\");\n }\nel\
+se\n {\n `cp $nb_o $con_o`;\n }\n\n\n`cp $con\
+_o $out`;\nif ( !-e $out)\n {\n print \"Tree C\
+omputation failed [FAILED]\\n\";\n &my_exit (EX\
+IT_FAILURE);\n }\nelsif ($n>1)\n {\n print \"\
+\\nOutput Bootstrapped Tree: $out\\n\";\n $avg=\
+`t_coffee -other_pg seq_reformat -in $out -action \
++avg_bootstrap`;\n $avg=~s/\\n//g;\n print \\
+"$avg\\n\";\n }\nelse\n {\n print \"\\nOutput\
+ Tree: $out\\n\";\n }\n\nopen (F, \"$out\");\nwhi\
+le (<F>)\n {\n \n $tree.=$_;\n }\nclose (F\
+);\n$tree=~s/\\n//g;\nprint \"BPH: $tree\\n\";\n\n\
+\n&my_exit (EXIT_SUCCESS);\n\nsub my_exit \n {\n \
+ my $m=@_[0];\n &clean_vtmpnam();\n exit (\
+$m);\n }\nsub vtmpnam \n {\n my $file;\n\n\n \
+ $ntmp++;\n $file=\"tmp4msa2bootstrap.$rseed.\
+$$.$ntmp\";\n \n push (@tmpfile, $file);\n \
+ return $file;\n }\nsub clean_vtmpnam \n {\n \
+ my $t;\n foreach $t (@tmpfile)\n {\n if (\
+ -e $t){unlink ($t)};\n }\n }\n","use Env;\n\
+$seq_reformat=\"t_coffee -other_pg seq_reformat \"\
+;\n$VersionTag=\"1.00\";\n$step=1;\n$unset=\"\";\n\
+$scoreT1=$scoreT2=$nseqT=$dp_limit=$unset;\n@tl=()\
+;\nchomp($tc_version=`t_coffee -version`);$tc_vers\
+ion=~s/PROGRAM: //;\n\n\nprint STDERR \"\\n*******\
+**************************************************\
+********\";\nprint STDERR \"\\n* HIGH LE\
+VEL PROGRAM: T-COFFEE_DPA Version $VersionTag\";\n\
+print STDERR \"\\n* LOW LEVEL PROGRAM: \
+$tc_version \";\nprint STDERR \"\\n***************\
+**************************************************\
+\";\n\nif (!@ARGV)\n {\n print \"t_coffee_dpa \
+accepts every t_coffee_flag.\\nType t_coffee to ob\
+tain a list\\n\";\n print \"Requires $TC_VERSIO\
+N\\n\";\n print \"Requires \";\n print \"t_c\
+offee_dpa specific flags:\\n\";\n print \"\\t-d\
+pa_master_aln....................Master alignment:\
+ provided OR computed\\n\";\n print \"\\t-dpa_m\
+aster_aln....................By default, Computed \
+with t_coffee -very_fast\\n\";\n print \"\\t-dp\
+a_master_aln=<file>.............Use file, (must be\
+ an aln in Fasta or ClustalW\\n\";\n print \"\\\
+t-dpa_master_aln=<program>..........Compute aln wi\
+th pg -in seq -out aln`\\n\";\n print \"\\t-dpa\
+_maxnseq.......................Maximum number of s\
+equences in subgroups\\n\";\n print \"\\t-dpa_m\
+in_score1....................Minimum Id for two se\
+quences to be grouped in ref_aln\\n\";\n print \
+\"\\t-dpa_min_score2....................Minimum Id\
+ within a subgroup\\n\";\n print \"\\t-dpa_debu\
+g.........................Keep Tmp File (for debug\
+ purpose)\\n\\n\";\n \n exit (0);\n }\nfore\
+ach $arg (@ARGV)\n {\n $arg_list.=\" $arg\";\n\
+ }\n$arg_list=~s/[=,;]/ /g;\n\n\n($seq0, $arg_lis\
+t)=&extract_val_from_arg_list(\"^\",$arg_list, \"S\
+PLICE\",\"unset\");\n($seq1, $arg_list)=&extract_v\
+al_from_arg_list(\"-seq\",$arg_list, \"SPLICE\",\"\
+unset\");\n($seq2, $arg_list)=&extract_val_from_ar\
+g_list(\"-in\",$arg_list, \"KEEP\",\"unset\");\n($\
+seq3, $arg_list)=&extract_val_from_arg_list(\"-inf\
+ile\",$arg_list, \"SPLICE\",\"unset\");\n($prf, $\
+arg_list)=&extract_val_from_arg_list(\"-profile\",\
+$arg_list, \"SPLICE\",\"unset\");\n\n$gl{'Seq'}=$s\
+eq=&vtmpnam();#file containing all the sequences\n\
+\n #1-remove sequences from -in\nif ( $arg_list \
+=~/\\-in\\b/)\n {\n my $save, $name;\n whil\
+e($arg_list=~/\\-in\\b[^-]+(\\bS[\\w.]+)/)\n \
+{\n $name=$1;$name=~s/^.//;\n if ( !-e $name){$sav\
+e.=\" S$name \";}\n\n $arg_list=~s/S$name/ /;\n \
+ }\n $arg_list=~s/\\-in\\b/\\-in $save /;\n \
+}\n #2-prepare \n\nif (!($arg_list=~/\\-outorder\
+/))\n {\n \n $output_cl .=\" -outorder=$seq\
+\";\n }\n@output_flag=(\"-output\",\"-outfile\", \
+\"-run_name\", \"-outorder\"); \nforeach $v1 (@out\
+put_flag)\n {\n ($v2, $arg_list)=&extract_val_\
+from_arg_list($v1,$arg_list, \"SPLICE\",\"unset\")\
+;\n if ($v2 ne \"\")\n {\n\n if ($v1 eq \"\
+-run_name\"){$run_name=$v2;$output_cl .=\" $v1 $v2\
+ \";}\n elsif ( $v1 eq \"-outorder\")\n {\n \
+if ( $v2 eq \"input\"){$v2=$seq;}\n $outorder=\
+$v2;$output_cl .=\" $v1 $v2 \";\n }\n else\n {\
+\n $output_cl .=\" $v1 $v2 \";\n }\n }\\
+n }\n\n\n($dpa_master_aln, $arg_list) =&extract_v\
+al_from_arg_list(\"-dpa_master_aln\",$arg_list, \"\
+SPLICE\", \"t_coffee\");\n$dpa_master_aln=~s/\\s//\
+g;\n($nseqT, $arg_list) =&extract_val_fr\
+om_arg_list(\"-dpa_maxnseq\",$arg_list, \"SPLICE\"\
+, 30);\n($scoreT1, $arg_list) =&extract_va\
+l_from_arg_list(\"-dpa_min_score1\",$arg_list, \"S\
+PLICE\", 80);\n($scoreT2, $arg_list) =&ext\
+ract_val_from_arg_list(\"-dpa_min_score2\" ,$ar\
+g_list, \"SPLICE\", 30);\n($dpa_limit, $arg_list) \
+ =&extract_val_from_arg_list(\"-dpa_limit\" \
+ ,$arg_list, \"SPLICE\", 0);\n($dpa_delta_id,\
+ $arg_list) =&extract_val_from_arg_list(\"-dpa_\
+delta_id\" ,$arg_list, \"SPLICE\", 1);\n($d\
+pa_debug, $arg_list) =&extract_val_from_arg_\
+list(\"-dpa_debug\" ,$arg_list, \"SPLICE\
+\", 0);\n\n\n$in_seq=$seq0.\" \".$seq1.\" \".$seq2\
+.\" \".$seq3;\n$in_prf=(($prf ne $unset)?\"$prf \"\
+:\"\");\n&exit_dpa (($in_seq eq \"\" && $in_prf eq\
+ \"\")?1:0, \"ERROR: You did not Provide any seque\
+nces. Use the -seq flag [FATAL: t_coffee_dpa]\\n\"\
+, EXIT_FAILURE);\n\n\nprint STDERR \"\\nSTART DPA \
+COMPUTATION\";\n\n\n\nif ($in_seq=~/\\S+/)\n {\n \
+ \n print STDERR \"\\n Step $step: Gather all\
+ the sequences into the tmp file: [$seq]\";$step++\
+; \n &my_system (\"t_coffee $in_seq -convert -q\
+uiet -output fasta_seq -outfile=$seq -maxnseq 0\")\
+;\n }\n\nif ( !-e $seq){$seq=\"\";}\n\nif ($in_pr\
+f=~/\\S+/)\n {\n $seq_in_type=\"profile\"; \n \
+ $seq.= $in_prf; \n }\nif ($seq eq \"\"){ &exit\
+_dpa (1, \"\\nERROR: No Sequence FOund. Provide Se\
+quences with the -seq flag [FATAL: t_coffee_dpa]\"\
+, EXIT_FAILURE);}\n\n \n\nif ( $run_name)\n {\n \
+ $suffix=$run_name;\n }\nelsif ($in_seq=~/\\b(S[\
+\\w.]+\\b)/)\n {\n my $suffix1, $sufffix2;\n \
+ $suffix1=$suffix2=$1;\n $suffix2=~s/^S//;\n \
+ if ( -e $suffix1){$suffix=$suffix1;}\n elsif \
+( -e $suffix2){$suffix=$suffix2;}\n else\n \
+ {\n $suffix=&vtmpnam(); \n }\n $suffix=~s\
+/\\.\\w+//;\n }\n\nelse\n {\n $suffix=&vtmpna\
+m();\n }\n\n\nif (!$run_name){$output_cl.=\" -run\
+_name $suffix \";}\n\n\n$gl{'Tree'}=&seq2dpa_tree \
+($seq, \"$suffix.dpadnd\");\n\nprint STDERR \"\\n \
+Step $step: Prepare guide tree: $gl{'Tree'}\";$ste\
+p++;\n\nprint STDERR \"\\n Step $step: Identify an\
+d Align Closely Related Groups\";$step++;\n%gl=&ma\
+ke_one_pass (0, $scoreT1,\"Align\",%gl);\n\nprint \
+STDERR \"\\n Step $step: Make Multiple Group Align\
+ment\";$step++;\nwhile (!%gl ||$gl{'Ng'}>$nseqT)\n\
+ {\n %gl=&make_one_pass ($nseqT, $scoreT2,\"t_\
+coffee\",%gl);\n if ( $gl{'Newgroups'}==0){$sco\
+reT2--;} \n }\nprint STDERR \"\\n Step $step: \
+Make The Final Alignment\";$step++;\n\n\n$arg_list\
+ .=$output_cl;\n\n\n%gl=&tree2group (0,0, %gl);\n$\
+gl{$gl{'0'}{'File'}}{'Output'}=\"\";\n$a=0;\n&alig\
+n_groups (\"t_coffee\",'0', $arg_list, \" \", %gl)\
+;\n\n\n\nif ( !$dpa_keep_tmpfile){&clean_tmp_file \
+(@tl);}\n\n\n\nsub seq2dpa_tree \n {\n my $seq\
+=@_[0];\n my $newtree=@_[1];\n my $aln=&vtmp\
+nam ();\n\n &my_system (\"t_coffee -special_mod\
+e quickaln -in $seq -outfile $aln -quiet\");\n \
+&my_system (\"$seq_reformat -in $aln -action +aln2\
+tree +tree2dpatree -output newick >$newtree\");\n \
+ return $newtree;\n } \nsub seq2dpa_tree_old \n\
+ {\n my $aln=@_[0];\n my $newtree=@_[1];\n \
+ \n \n &my_system(\"$seq_reformat -in $aln\
+ -action +seq2dpatree -output newick > $newtree\")\
+;\n return $newtree;\n }\nsub aln2dpa_tree \n \
+ {\n my $aln=@_[0];\n my $newtree=&vtmpnam()\
+;\n \n &my_system(\"$seq_reformat -in $aln -\
+action +aln2tree +tree2dpatree -output newick > $n\
+ewtree\");\n return $newtree;\n }\nsub group_f\
+ile2ngroups\n {\n my $file=@_[0];\n my $n;\\
+n \n open ( F, $file);\n while (<F>)\n \
+ {\n $n+=/\\>/;\n }\n close (F);\n re\
+turn $n;\n }\n\nsub make_one_pass\n {\n my ($\
+N, $ID,$pg, %gl)=@_;\n my $a;\n\n %gl=&tree2\
+group ($N,$ID,%gl);\n if (!$gl{'Newgroups'}){re\
+turn %gl;}\n else\n {\n for ( $a=0; $a< $n\
+g; $a++)\n {\n if ($gl{$gl{$a}{'File'}}{'Ng'\
+}>1){&display_group($a, %gl);}\n &align_groups\
+ ($pg, $a, $arg_list, \" -quiet=quiet \", %gl);\n \
+ }\n return %gl;\n }\n }\n\nsub tree2group \
+\n {\n my ($N, $ID, %gl)=@_;\n my $prefix=&\
+vtmpnam();\n my $group_file=&vtmpnam();\n my\
+ $file;\n my $oldtree=&vtmpnam();\n my $n;\n\
+ my $tree;\n\n\n if ( $gl{'Ng'}==1){return %\
+gl;}\n $tree=$gl{'Tree'}; \n \n #1 extrac\
+t the groups\n &my_system (\"$seq_reformat -in \
+$tree -action +tree2group $N $ID $prefix > $group_\
+file\");\n $n=group_file2ngroups($group_file);\\
+n \n \n $gl{'Newgroups'}=1;\n if ( $n=\
+=$gl{'Ng'})\n {\n $gl{'Newgroups'}=0;\n retur\
+n %gl;\n }\n $gl{'Iteration'}++;\n $gl{\
+'MaxNseq'}=$N;$gl{'MinID'}=$ID;\n $gl{'GroupFil\
+e'}=$group_file;$gl{'Ng'}=$ng=0;\n #2 Process t\
+he group list into the hash\n open (F, $group_f\
+ile);\n while (<F>)\n {\n $gl{'File'}.=$_;\
+\n if (/\\>/)\n {\n $line=$_;\n $line=~s\
+/\\>//;\n @list=($line=~/(\\S+)/g);\n $fil\
+e=$gl{$ng}{'File'}=shift @list;\n $gl{$file}{'\
+Output'}=$file;\n \n $gl{$file}{'Ng'}=$#li\
+st+1;\n if ($gl{$file}{'Ng'}>1){ $gl{$file}{'T\
+list'}=$gl{$file}{'Alist'}=\"(\";}\n foreach $\
+l (@list)\n {\n \n $gl{$file}{'List'}.=\" $\
+l \";\n \n if (!$gl{$l}{'Tlist'})\n {\n \
+$gl{$l}{'Tlist'}=\"$l\";\n $gl{$l}{'Alist'}=\\
+"$l\";\n $gl{$l}{'Nseq'}=1;\n $gl{$l}{'N\
+g'}=1;\n }\n $gl{$file}{'Tlist'}.=\"$gl{$l}{'T\
+list'},\";\n $gl{$file}{'Alist'}.=\"$gl{$l}{'Tlis\
+t'}|\";\n $gl{$file}{'Nseq'}+=$gl{$l}{'Nseq'};\n \
+ }\n \n\n chop($gl{$file}{'Tlist'});c\
+hop($gl{$file}{'Alist'});\n if ($gl{$file}{'Ng\
+'}>1){$gl{$file}{'Tlist'}.=\")\"; $gl{$file}{'Alis\
+t'}.=\");\";}\n $ng++;\n } \n }\n $g\
+l{'Ng'}=$ng;\n close (F);\n \n #3 Update \
+the old tree with the new groups\n $gl{'Tree'}=\
+&vtmpnam();\n &my_system (\"$seq_reformat -in $\
+tree -action +collapse_tree $group_file -output ne\
+wick > $gl{'Tree'}\");\n \n return %gl;\n }\
+\n\nsub display_group \n {\n my ($g,%gl)=@_;\n\
+ my $f;\n \n if ( $g==-1)\n {\n prin\
+t STDERR \"\\nIteration $gl{'Iteration'} [MaxN=$gl\
+{'MaxNseq'}][MinID=$gl{'MinID'}]\";\n }\n \
+else\n {\n\n $f=$gl{$g}{'File'};\n $action=($\
+gl{$f}{'Ng'}==1 || $gl{'Iteration'}==1)?\"KEEP \"\
+:\"ALIGN \";\n print STDERR \"\\n\\t[$actio\
+n][MaxN=$gl{'MaxNseq'}][MinID=$gl{'MinID'}][File $\
+f][Nseq=$gl{$f}{'Nseq'}][Ngroups=$gl{$f}{'Ng'}][$g\
+l{$f}{'Alist'}]\";\n }\n }\n \n\n\nsub \
+align_groups\n {\n my ($pg, $g, $arg, $extra_a\
+rg,%gl)=@_;\n my $f;\n my $Output,$Outflag;\\
+n \n \n $f=$gl{$g}{'File'};\n $Output=\
+($gl{$f}{'Output'});\n \n if ( $pg eq \"Alig\
+n\")\n {\n if ( !-e $f)\n {\n $command=\
+\"$seq_reformat -in $gl{'Seq'} -action +extract_a\
+ln $gl{'GroupFile'}\";\n if ($gl{$f}{'Ng'}>1)\\
+n {\n &my_system ($command);\n $command=\"\
+t_coffee -special_mode quick_aln S$f -outfile=$Ou\
+tput -quiet\";\n }\n }\n else \n {$comma\
+nd=\"\";}\n }\n elsif ( -e $f)\n { \n\
+ $Outflag=($Output)?\"-outfile=$Output\":\"\";\n $\
+command=\"$pg -infile $f $Outflag -quiet stdout $a\
+rg $extra_arg -maxnseq 0 -convert -quiet stdout\";\
+\n }\n elsif ( $gl{$f}{'Ng'}==1)\n {\\
+n $action=($dpa_debug)?\"cp\":\"mv\";\n $command=\\
+"$action $gl{$f}{'List'} $Output\";\n }\n \
+else\n {\n $Outflag=($Output)?\"-outfile=$Out\
+put\":\"\";\n $command=\"$pg -profile $gl{$f}{'Lis\
+t'} $Outflag $arg $extra_arg -maxnseq 0\";\n \
+}\n \n &my_system ($command);\n return $o\
+utfile;\n }\n \nsub my_system \n {\n my $c\
+ommand=@_[0];\n my $force=@_[1];\n my $statu\
+s;\n\n if ( $dpa_debug) {print STDERR \"\\nCOMM\
+AND: $command\";}\n $status=system ($command);\\
+n\n if (!$force)\n {\n &exit_dpa (($stat\
+us==1), \"Failed in Command:\\n$command\\n[FATAL: \
+t_coffee_dpa]\\n\", EXIT_FAILURE);\n }\n \
+\n return $status;\n }\n\nsub vtmpnam\n {\n \
+ my $prefix=@_[0];\n my $tmp_file_name;\n\n \
+ $tmp_prefix=($prefix)?$prefix:\"dpa_tmp_file_$$\"\
+;\n \n $tmp_count++;\n $tmp_file_name=\"$t\
+mp_prefix\".\"$tmp_count\";\n $tl[$#tl+1]=$tmp_\
+file_name;\n return $tmp_file_name;\n }\n\nsub\
+ clean_tmp_file\n {\n\n my $list;\n my $fil\
+e;\n \n if ($dpa_debug){return;}\n $list=\
+vtmpnam();\n `ls -1 | grep $tmp_prefix>$list`;\\
+n \n open (F,$list);\n while ( <F>)\n \
+ {\n $file=$_;\n chop $file;\n if ( -e $file){unl\
+ink $file;}\n }\n close (F);\n unlink $\
+list;\n }\n\n\nsub exit_dpa\n {\n my $condition\
+=@_[0];\n my $error_msg=@_[1];\n my $exit_value=\
+@_[2];\n if ( $condition)\n {\n print \"$\
+error_msg\\n\";\n exit ($exit_value);\n }\\
+n else\n {\n return;\n }\n \n}\nsub e\
+xtract_val_from_arg_list\n {\n my $arg=@_[0];\\
+n my $arg_list=@_[1];\n my $keep_flag=@_[2];\
+\n my $default_value=@_[3];\n my $val=\"\";\\
+n \n #protect\n $arg_list=~s/\\s-/ \\@/g;\
+\n $arg=~s/-/\\@/g;\n \n #search\n if \
+($arg eq \"^\")\n {\n $arg_list=~/^([^@]*)/;\\
+n $val=$1;\n }\n else\n {$arg_list=~/\
+$arg ([^@]*)/;$val=$1;}\n \n #remove trailin\
+g spaces\n $val=~s/\\s*$//;\n \n #remove \
+the parsed sequence if needed\n if (($val ne \"\
+\") && $keep_flag ne \"KEEP\")\n {\n if ( $ar\
+g eq \"^\"){$arg_list=~s/$val/ /;}\n else {$arg_li\
+st=~s/($arg [^@]*)/ /;}\n }\n \n #unprotec\
+t\n $arg_list=~s/\\@/-/g;\n $arg=~s/\\@/-/g;\
+\n \n if (($val eq \"\") && $default_value n\
+e \"unset\"){$val=$default_value;}\n \n retu\
+rn $val, $arg_list;\n }\n$program=\"T-COFFEE (r25\
+3)\";\n\n","\n$DEBUG=1;\n$dpa_nseq=10;\n$dpa_sim=0\
+;\nif (!@ARGV)\n {\n `t_coffee`;\n exit (0)\
+;\n }\nforeach $arg (@ARGV)\n {\n $arg_list.=\
+\" $arg\";\n }\n$max_nseq=10;\n($seq0, $arg_list)\
+=&extract_val_from_arg_list(\"^\",$arg_list);\n($s\
+eq1, $arg_list)=&extract_val_from_arg_list(\"-seq\\
+",$arg_list);\n($seq2, $arg_list)=&extract_val_fro\
+m_arg_list(\"-in\",$arg_list, \"KEEP\");\n($seq3, \
+$arg_list)=&extract_val_from_arg_list(\"-infile\",\
+$arg_list);\n$in_seq=$seq0.\" \".$seq1.\" \".$seq2\
+.\" \".$seq3;\n\n$seq=vtmpnam();\n`t_coffee $in_se\
+q -convert -output fasta_seq -outfile=$seq`;\n\n\n\
+($dpa_nseq, $arg_list)=&extract_val_from_arg_list(\
+\"-dpa_nseq\",$arg_list);\n($master_aln, $arg_list\
+)=&extract_val_from_arg_list(\"-master_aln\",$arg_\
+list);\n($sim_matrix, $arg_list)=&extract_val_from\
+_arg_list(\"-sim_matrix\",$arg_list);\n($core_seq,\
+ $arg_list)=&extract_val_from_arg_list(\"-core_seq\
+\",$arg_list);\n($dpa_sim, $arg_list)=&extract_val\
+_from_arg_list(\"-dpa_sim\",$arg_list);\n($run_nam\
+e, $arg_list)=&extract_val_from_arg_list(\"-run_na\
+me\",$arg_list);\n($output, $arg_list)=&extract_va\
+l_from_arg_list(\"-output\",$arg_list);\n\n\n\nif \
+(!$sim_mat && !$master_aln)#Compute the fast align\
+ment\n {\n $ref_aln=vtmpnam();\n `t_coffee \
+-seq=$seq -very_fast -outfile=$ref_aln -quiet`;\n \
+ \n }\n\nif (!$sim_mat)\n {\n $sim_mat=vtmp\
+nam();\n `seq_reformat -in $ref_aln -output sim\
+ > $sim_mat`;\n }\n\nif ( !$core_seq)\n {\n $\
+core_seq=vtmpnam();\n `seq_reformat -in $ref_al\
+n -action +trimTC N$max_nseq -output fasta_seq > $\
+core_seq`;\n }\n@core_name=`seq_reformat -in $cor\
+e_seq -output name `; \n\n@tot_name=`seq_reformat \
+-in $seq -output name `;\n\nforeach $s (@core_name\
+){$s=~s/\\s//g;$hcore{$s}=1;}\nforeach $s (@tot_na\
+me){$s=~s/\\s//g;}\nprint STDERR \"T-Coffee_dpa:\\\
+n\";\nprint STDERR \"\\tTOTAL SEQ: @tot_name\\n\"\
+;\nprint STDERR \"\\tCHOSEN SEQ: @core_name\\n\";\\
+n\n\n\nopen (F, $sim_mat);\nwhile ( <F>)\n {\n \
+ @l=($_=~/(\\b[\\S]+\\b)/g);\n if (($l[0] eq \"\
+TOP\" || $l[0] eq \"BOT\"))\n {\n $s1=$l[1];$\
+s2=$l[2];$v=$l[3];\n if ($hcore{$s1} && !$hcore{$s\
+2})\n {\n if (!$hseq{$s2}{\"sim\"} || $v>$hs\
+eq{$s2}{\"sim\"})\n {\n $hseq{$s2}{\"sim\"}\
+=$v;$hseq{$s2}{\"seq\"}=$s1;\n }\n }\n \
+ }\n }\nclose (F);\nforeach $s (@tot_name)\n {\\
+n\n if ( !$hseq{$s}{\"seq\"}){;}\n else\n \
+ {\n $s2=$hseq{$s}{\"seq\"};\n $v=$hseq{$s}{\"si\
+m\"};\n \n if ($v>$dpa_sim)\n {\n $hseq{$s}\
+{'used'}=1;\n $seq_list{$s2}{$seq_list{$s2}{'n\
+seq'}++}=$s;\n }\n }\n }\nforeach $s (@cor\
+e_name){$seq_list{$s}{$seq_list{$s}{'nseq'}++}=$s;\
+$hseq{$s}{'used'}=1;}\nforeach $s (@tot_name){if (\
+!$hseq{$s}{'used'}){$seq_list{'unused'}{$seq_list{\
+'unused'}{'nseq'}++}=$s;}}\n\n\n$n=0;\nforeach $s \
+(@core_name)\n {\n $ng++;\n $n=$seq_list{$s\
+}{'nseq'};\n for (@g_list=(), $a=0; $a<$n; $a++\
+){@g_list=(@g_list,$seq_list{$s}{$a});}\n\n $g_\
+seq=vtmpnam();\n $g_aln=vtmpnam();\n \n p\
+rint STDERR \"Group $ng: $#g_list Seq: @g_list: \"\
+;\n \n \n `seq_reformat -in $seq -action \
++lower +keep_name +extract_seq @g_list -output fa\
+sta_seq > $g_seq`;\n \n \n if ( $#g_list=\
+=0)\n {\n print STDERR \"[No aln]\\n\";\n $g_\
+aln=$g_seq;\n }\n elsif ($#g_list<$max_nse\
+q) \n {\n print STDERR \"[t_coffee]\\n\";\n `\
+t_coffee $g_seq -outfile=$g_aln -quiet $arg_list`;\
+\n }\n else\n {\n print STDERR \"[t_c\
+offee_dpa]\\n\";\n `t_coffee_dpa2 $g_seq -outfile=\
+$g_aln $arg_list -sim_matrix $sim_matrix -dpa_nseq\
+ $dpa_nseq`;\n }\n @profile_list=(@profile\
+_list, $g_aln);\n }\n\n\nprint \"UNUSED $seq_list\
+{'unused'}{'nseq'}\";\n\nif ($seq_list{'unused'}{'\
+nseq'})\n {\n $prf=vtmpnam();\n \n \
+ `t_coffee -profile @profile_list $arg_list -out\
+file=$prf -quiet`;\n $n=$seq_list{\"unused\"}\
+{'nseq'};\n $new_seq=vtmpnam();\n $new_p\
+rf=vtmpnam();\n for ($a=0; $a<$n-1; $a++)\n {\
+\n $s=$seq_list{\"unused\"}{$a};\n print STDER\
+R \"\\nADD Sequence $s\";\n \n `seq_reformat -\
+in $seq -action +lower +keep_name +extract_seq $s \
+ -output fasta_seq > $new_seq`;\n `t_coffee -pro\
+file $prf $new_seq $arg_list -outfile=$new_prf`;\n\
+ `cp $new_prf $prf`;\n }\n $s=$seq_list{\"u\
+nused\"}{$a};\n `seq_reformat -in $seq -actio\
+n +lower +keep_name +extract_seq $s -output fasta\
+_seq > $new_seq`;\n @profile_list=($prf, $new\
+_seq);\n }\n \n \nif ($run_name){$arg_l\
+ist.=\" -run_name $run_name\";}\nelse \n {\n $\
+in_seq=~/([\\w-]+)/;\n $arg_list.=\" -run_name \
+$1\";\n }\nif ( $output){$arg_list.=\" -output $o\
+utput \";}\n\n`t_coffee -profile @profile_list $ar\
+g_list`;\n\n\n&clean (@tmp_file_list);\n\n\nsub vt\
+mpnam\n {\n my $tmp_file_name;\n $tmp_name_\
+counter++;\n $tmp_file_name=\"tmp_file_$tmp_nam\
+e_counter\\_Pid$$\";\n $tmp_file_list[$ntmp_fil\
+e++]=$tmp_file_name;\n return $tmp_file_name;\n\
+ }\nsub clean\n {\n my @fl=@_;\n my $file;\n \
+return;\n\n foreach $file ( @fl)\n {\n if\
+ ( -e $file){unlink($file);}\n }\n}\nsub extrac\
+t_val_from_arg_list\n {\n my $arg=@_[0];\n \
+my $arg_list=@_[1];\n my $keep_flag=@_[2];\n \
+ #protect\n $arg_list=~s/\\s-/ \\@/g;\n $arg\
+=~s/-/\\@/g;\n \n #search\n if ($arg eq \\
+"^\")\n {\n $arg_list=~/^([^@]*)/;\n $val=$1;\
+\n }\n else\n {$arg_list=~/$arg ([^@]\
+*)/;$val=$1;}\n \n #remove the parsed sequen\
+ce if needed\n if ($val && $keep_flag ne \"KEEP\
+\")\n {\n if ( $arg eq \"^\"){$arg_list=~s/$v\
+al/ /;}\n else {$arg_list=~s/($arg [^@]*)/ /;}\n \
+ }\n \n #unprotect\n $arg_list=~s/\\@/-/g\
+;\n $arg=~s/\\@/-/g;\n \n return $val, $a\
+rg_list;\n }\n\n","use Env;\nuse FileHandle;\nuse\
+ Cwd;\nuse File::Path;\nuse Sys::Hostname;\n\nour \
+$PIDCHILD;\nour $ERROR_DONE;\nour @TMPFILE_LIST;\n\
+our $EXIT_FAILURE=1;\nour $EXIT_SUCCESS=0;\n\nour \
+$REFDIR=getcwd;\nour $EXIT_SUCCESS=0;\nour $EXIT_F\
+AILURE=1;\n\nour $PROGRAM=\"tc_generic_method.pl\"\
+;\nour $CL=$PROGRAM;\n\nour $CLEAN_EXIT_STARTED;\n\
+our $debug_lock=$ENV{\"DEBUG_LOCK\"};\nour $debug_\
+cmd_exec=$ENV{\"DEBUG_CMD_EXEC\"};\nour $LOCKDIR=$\
+ENV{\"LOCKDIR_4_TCOFFEE\"};\nif (!$LOCKDIR){$LOCKD\
+IR=getcwd();}\nour $ERRORDIR=$ENV{\"ERRORDIR_4_TCO\
+FFEE\"};\nour $ERRORFILE=$ENV{\"ERRORFILE_4_TCOFFE\
+E\"};\n&set_lock ($$);\nif (isshellpid(getppid()))\
+{lock4tc(getppid(), \"LLOCK\", \"LSET\", \"$$\\n\"\
+);}\n \n\n\n\n\nour $BLAST_MAX_NRUNS=2;\nour \
+$COMMAND;\nour $PIDCHILD;\n\n$REF_EMAIL=\"\";\n$tm\
+p_dir=\"\";\n$init_dir=\"\";\n\n\n$test=0;\nif ($t\
+est==1)\n {\n $SERVER=\"NCBI\";\n $query=$A\
+RGV[0];\n $hitf=$ARGV[1];\n %s=read_fasta_se\
+q($query);\n @sl=keys(%s);\n &blast_xml2prof\
+ile (\"xx\", $s{$sl[0]}{seq},$maxid,$minid,$mincov\
+, $hitf);\n myexit ($EXIT_FAILURE);\n }\n\nfor\
+each $v(@ARGV){$cl.=\"$v \";}\n$COMMAND=$cl;\n($mo\
+de)=&my_get_opt ( $cl, \"-mode=\",1,0);\n\n($A)=(&\
+my_get_opt ( $cl, \"-name1=\",0,0));\n($B)=(&my_ge\
+t_opt ( $cl, \"-name2=\",0,0));\n($TMPDIR)=(&my_ge\
+t_opt ( $cl, \"-tmpdir=\",0,0));\n($CACHE)=(&my_ge\
+t_opt ( $cl, \"-cache=\",0,0));\n($SERVER)=((&my_g\
+et_opt ( $cl, \"-server=\",0,0)));\n($EMAIL)=((&my\
+_get_opt ( $cl, \"-email=\",0,0)));\n\nif (!$A){$A\
+=\"A\";}\nif (!$B){$B=\"B\";}\n\n\nif (!$TMPDIR)\n\
+ {\n $HOME=$ENV{HOME};\n if ($ENV{TMP_4_TCO\
+FFEE}){$TMPDIR=$ENV{TMP_4_TCOFFEE};}\n else{$TM\
+PDIR=\"$HOME/.t_coffee/tmp/\";}\n }\nif ( ! -d $T\
+MPDIR)\n {\n mkdir $TMPDIR;\n }\nif ( ! -d $T\
+MPDIR)\n {\n print \"ERROR: Could not create t\
+emporary dir: $TMPDIR\\n\";\n myexit ($EXIT_FAI\
+LURE);\n }\n\n$EMAIL=~s/XEMAILX/\\@/g;\nif (!$EMA\
+IL)\n {\n if ($ENV{EMAIL_4_TCOFFEE}){$EMAIL=$E\
+NV{EMAIL_4_TCOFFEE};}\n elsif ($ENV{EMAIL}){$EM\
+AIL=$ENV{EMAIL};}\n else {$EMAIL=$REF_EMAIL;}\n\
+ }\n\n($maxid,$minid,$mincov)=(&my_get_opt ( $cl,\
+ \"-maxid=\",0,0, \"-minid=\",0,0,\"-mincov=\",0,0\
+));\nif (!$cl=~/\\-maxid\\=/){$maxid=95;}\nif (!$c\
+l=~/\\-minid\\=/){$minid=35;}\nif (!$cl=~/\\-minco\
+v\\=/){$mincov=80;}\n\n\n\n\nif ($mode eq \"seq_ms\
+a\")\n {\n &seq2msa($mode,&my_get_opt ( $cl, \\
+"-infile=\",1,1, \"-method=\",1,2, \"-param=\",0,0\
+,\"-outfile=\",1,0, \"-database=\",0,0));\n }\nel\
+sif ( $mode eq \"tblastx_msa\")\n {\n &seq2tbl\
+astx_lib ($mode,&my_get_opt ( $cl, \"-infile=\",1,\
+1, \"-outfile=\",1,0));\n }\nelsif ( $mode eq \"t\
+blastpx_msa\")\n {\n &seq2tblastpx_lib ($mode,\
+&my_get_opt ( $cl, \"-infile=\",1,1, \"-outfile=\"\
+,1,0));\n }\nelsif ( $mode eq \"thread_pair\")\n \
+ {\n &seq2thread_pair($mode,&my_get_opt ( $cl, \
+\"-infile=\",1,1, \"-pdbfile1=\",1,1, \"-method=\"\
+,1,2,\"-param=\",0,0, \"-outfile=\",1,0, ));\n }\\
+nelsif ( $mode eq \"pdbid_pair\")\n {\n &seq2p\
+dbid_pair($mode,&my_get_opt ( $cl, \"-pdbfile1=\",\
+1,0, \"-pdbfile2=\",1,0, \"-method=\",1,2,\"-param\
+=\",0,0, \"-outfile=\",1,0, ));\n }\nelsif ( $mod\
+e eq \"pdb_pair\")\n {\n &seq2pdb_pair($mode,&\
+my_get_opt ( $cl, \"-pdbfile1=\",1,1, \"-pdbfile2=\
+\",1,1, \"-method=\",1,2,\"-param=\",0,0, \"-outfi\
+le=\",1,0, ));\n }\nelsif ( $mode eq \"profile_pa\
+ir\")\n {\n &seq2profile_pair($mode,&my_get_o\
+pt ( $cl, \"-profile1=\",1,1, \"-profile2=\",1,1, \
+\"-method=\",1,2,\"-param=\",0,0, \"-outfile=\",1,\
+0 ));\n }\nelsif ($mode eq \"pdb_template_test\")\
+\n {\n &blast2pdb_template_test ($mode,&my_get\
+_opt ( $cl, \"-infile=\",1,1));\n\n }\nelsif ($mo\
+de eq \"psi_template_test\")\n {\n &psiblast2p\
+rofile_template_test ($mode,&my_get_opt ( $cl, \"-\
+seq=\",1,1,\"-blast=\",1,1));\n\n }\n\nelsif ( $m\
+ode eq \"pdb_template\")\n {\n &blast2pdb_temp\
+late ($mode,&my_get_opt ( $cl, \"-infile=\",1,1, \\
+"-database=\",1,0, \"-method=\",1,0, \"-outfile=\"\
+,1,0,\"-pdb_type=\",1,0));\n }\n\nelsif ( $mode e\
+q \"profile_template\")\n {\n \n &psiblast2\
+profile_template ($mode,&my_get_opt ( $cl, \"-infi\
+le=\",1,1, \"-database=\",1,0, \"-method=\",1,0, \\
+"-outfile=\",1,0));\n }\nelsif ( $mode eq \"psipr\
+ofile_template\")\n {\n &psiblast2profile_temp\
+late ($mode,&my_get_opt ( $cl, \"-infile=\",1,1, \\
+"-database=\",1,0, \"-method=\",1,0, \"-outfile=\"\
+,1,0));\n }\nelsif ( $mode eq \"RNA_template\")\n\
+ {\n &seq2RNA_template ($mode,&my_get_opt ( $c\
+l, \"-infile=\",1,1, \"-outfile=\",1,0));\n }\nel\
+sif ( $mode eq \"tm_template\")\n {\n &seq2tm_\
+template ($mode, \"\", &my_get_opt ( $cl, \"-infil\
+e=\",1,1,\"-arch=\",1,1,\"-psv=\",1,1, \"-outfile=\
+\",1,0,));\n }\nelsif ( $mode eq \"psitm_template\
+\")\n {\n &seq2tm_template ($mode,&my_get_opt \
+( $cl, \"-database=\",1,0, \"-infile=\",1,1, \"-ar\
+ch=\",1,1,\"-psv=\",1,1, \"-outfile=\",1,0,));\n \
+}\nelsif ( $mode eq \"ssp_template\")\n {\n &s\
+eq2ssp_template ($mode,&my_get_opt ( $cl, \"-infil\
+e=\",1,1,\"-seq=\",1,1,\"-obs=\",1,1, \"-outfile=\\
+",1,0));\n }\nelsif ( $mode eq \"psissp_template\\
+")\n {\n &seq2ssp_template ($mode,&my_get_opt \
+( $cl, \"-infile=\",1,1,\"-seq=\",1,1,\"-obs=\",1,\
+1, \"-outfile=\",1,0));\n }\n\nelsif ( $mode eq \\
+"rna_pair\")\n{\n &seq2rna_pair($mode,&my_get_o\
+pt ( $cl, \"-pdbfile1=\",1,1, \"-pdbfile2=\",1,1, \
+\"-method=\",1,2,\"-param=\",0,0, \"-outfile=\",1,\
+0, ));\n}\nelsif ( $mode eq \"calc_rna_template\")\
+\n{\n &calc_rna_template($mode,&my_get_opt ( $c\
+l, \"-infile=\",1,1,\"-pdbfile=\",1,1, \"-outfile=\
+\",1,0));\n}\nelse\n {\n myexit(flush_error( \\
+"$mode is an unknown mode of tc_generic_method.pl\\
+"));\n }\nmyexit ($EXIT_SUCCESS);\n\n\nsub seq2ss\
+p_template\n {\n my ($mode, $infile,$gor_seq,$go\
+r_obs,$outfile)=@_;\n my %s, %h;\n my $result;\n\
+ my (@profiles);\n &set_temporary_dir (\"set\",$\
+infile,\"seq.pep\");\n %s=read_fasta_seq (\"seq.p\
+ep\");\n\n \n open (R, \">result.aln\");\n \n \
+#print stdout \"\\n\";\n foreach $seq (keys(%s))\\
+n {\n \n open (F, \">seqfile\");\n \
+ $s{$seq}{seq}=uc$s{$seq}{seq};\n print (F \
+\">$s{$seq}{name}\\n$s{$seq}{seq}\\n\");\n cl\
+ose (F);\n $lib_name=\"$s{$seq}{name}.ssp\";\\
+n $lib_name=&clean_file_name ($lib_name);\n \
+ \n if ($mode eq \"ssp_template\"){&seq2go\
+r_prediction ($s{$seq}{name},$s{$seq}{seq}, \"seqf\
+ile\", $lib_name,$gor_seq, $gor_obs);}\n elsi\
+f ($mode eq \"psissp_template\")\n {\n &seq2msa_\
+gor_prediction ($s{$seq}{name},$s{$seq}{seq},\"seq\
+file\", $lib_name,$gor_seq, $gor_obs);\n }\n \n\
+ if ( !-e $lib_name)\n {\n myexit(flush_err\
+or(\"GORIV failed to compute the secondary structu\
+re of $s{$seq}{name}\"));\n myexit ($EXIT_FAILUR\
+E);\n }\n else\n {\n print stdout \"\\tProc\
+ess: >$s{$seq}{name} _E_ $lib_name \\n\";\n prin\
+t R \">$s{$seq}{name} _E_ $lib_name\\n\";\n }\n \
+ unshift (@profiles, $lib_name);\n }\n close\
+ (R);\n &set_temporary_dir (\"unset\",$mode, $met\
+hod,\"result.aln\",$outfile, @profiles);\n}\n\nsub\
+ seq2tm_template\n {\n my ($mode, $db, $infile,$\
+arch,$psv,$outfile)=@_;\n my %s, %h;\n my $resul\
+t;\n my (@profiles);\n &set_temporary_dir (\"set\
+\",$infile,\"seq.pep\");\n %s=read_fasta_seq (\"s\
+eq.pep\");\n\n \n open (R, \">result.aln\");\n \
+\n #print stdout \"\\n\";\n foreach $seq (keys(%\
+s))\n {\n open (F, \">seqfile\");\n p\
+rint (F \">$s{$seq}{name}\\n$s{$seq}{seq}\\n\");\n\
+ close (F);\n $lib_name=\"$s{$seq}{name}\
+.tmp\";\n $lib_name=&clean_file_name ($lib_na\
+me);\n\n if ($mode eq \"tm_template\")\n {\n \
+ &safe_system (\"t_coffee -other_pg fasta_seq2hmm\
+top_fasta.pl -in=seqfile -out=$lib_name -arch=$arc\
+h -psv=$psv\");\n }\n elsif ( $mode eq \"psit\
+m_template\")\n {\n &seq2msa_tm_prediction ($s{$\
+seq}{name},$s{$seq}{seq}, $db, \"seqfile\", $lib_n\
+ame,$arch, $psv);\n }\n if ( !-e $lib_name)\n\
+ {\n myexit(flush_error(\"RNAplfold failed to co\
+mpute the secondary structure of $s{$seq}{name}\")\
+);\n myexit ($EXIT_FAILURE);\n }\n else\n {\
+\n print stdout \"\\tProcess: >$s{$seq}{name} _T\
+_ $lib_name\\n\";\n print R \">$s{$seq}{name} _T\
+_ $lib_name\\n\";\n }\n unshift (@profiles, $\
+lib_name);\n }\n close (R);\n &set_temporary_\
+dir (\"unset\",$mode, $method,\"result.aln\",$outf\
+ile, @profiles);\n}\n\nsub seq2RNA_template\n {\n\
+ my ($mode, $infile,$outfile)=@_;\n my %s, %h, ;\
+\n my $result;\n my (@profiles);\n &set_tempora\
+ry_dir (\"set\",$infile,\"seq.pep\");\n %s=read_f\
+asta_seq (\"seq.pep\");\n\n \n open (R, \">resul\
+t.aln\");\n \n #print stdout \"\\n\";\n foreach\
+ $seq (keys(%s))\n {\n open (F, \">seqfile\
+\");\n print (F \">$s{$seq}{name}\\n$s{$seq}{\
+seq}\\n\");\n close (F);\n $lib_name=\"$\
+s{$seq}{name}.rfold\";\n $lib_name=&clean_fil\
+e_name ($lib_name);\n &safe_system (\"t_coffe\
+e -other_pg RNAplfold2tclib.pl -in=seqfile -out=$l\
+ib_name\");\n \n if ( !-e $lib_name)\n {\
+\n myexit(flush_error(\"RNAplfold failed to compu\
+te the secondary structure of $s{$seq}{name}\"));\\
+n myexit ($EXIT_FAILURE);\n }\n else\n {\n \
+ print stdout \"\\tProcess: >$s{$seq}{name} _F_ $\
+lib_name\\n\";\n print R \">$s{$seq}{name} _F_ $\
+lib_name\\n\";\n }\n unshift (@profiles, $lib\
+_name);\n }\n close (R);\n &set_temporary_dir\
+ (\"unset\",$mode, $method,\"result.aln\",$outfile\
+, @profiles);\n}\nsub psiblast2profile_template_te\
+st\n {\n my ($mode, $seq,$blast)=@_;\n my %s, %\
+h, ;\n my ($result,$psiblast_output,$profile_name\
+,@profiles);\n my $trim=0;\n my $maxid=100;\n m\
+y $minid=0;\n my $mincov=0;\n my $maxcov=100;\n \
+ \n %s=read_fasta_seq ($seq);\n open (R, \">resu\
+lt.aln\");\n \n #print stdout \"\\n\";\n foreac\
+h $seq (keys(%s))\n {\n \n open (F, \\
+">seqfile\");\n print (F \">$A\\n$s{$seq}{seq\
+}\\n\");\n close (F);\n $psiblast_output\
+=$blast;\n if ( -e $psiblast_output)\n {\n \
+%profile=blast_xml2profile($s{$seq}{name}, $s{$seq\
+}{seq},$maxid, $minid,$mincov,$psiblast_output);\n\
+\n\n \n $profile_name=\"$s{$seq}{name}.prf\";\\
+n $profile_name=&clean_file_name ($profile_name)\
+;\n unshift (@profiles, $profile_name);\n outp\
+ut_profile ($profile_name, \\%profile, $trim);\n \
+ print stdout \"\\tProcess: >$s{$seq}{name} _R_ $p\
+rofile_name [$profile{n} Seq.] [$SERVER/blast/$db]\
+[$CACHE_STATUS]\\n\";\n print R \">$s{$seq}{name\
+} _R_ $profile_name\\n\";\n }\n }\n close (R);\
+\n \n die;\n}\nsub psiblast2profile_template \n \
+ {\n my ($mode, $infile, $db, $method, $outfile)=\
+@_;\n my %s, %h, ;\n my ($result,$psiblast_outpu\
+t,$profile_name,@profiles);\n my $trim=0;\n &set\
+_temporary_dir (\"set\",$infile,\"seq.pep\");\n %\
+s=read_fasta_seq (\"seq.pep\");\n open (R, \">res\
+ult.aln\");\n \n #print stdout \"\\n\";\n forea\
+ch $seq (keys(%s))\n {\n open (F, \">seqfi\
+le\");\n print (F \">$A\\n$s{$seq}{seq}\\n\")\
+;\n close (F);\n $psiblast_output=&run_b\
+last ($s{$seq}{name},$method, $db, \"seqfile\",\"o\
+utfile\");\n \nif ( -e $psiblast_output)\n {\\
+n %profile=blast_xml2profile($s{$seq}{name}, $s{\
+$seq}{seq},$maxid, $minid,$mincov,$psiblast_output\
+);\n unlink ($psiblast_output);\n \n $profil\
+e_name=\"$s{$seq}{name}.prf\";\n $profile_name=&\
+clean_file_name ($profile_name);\n unshift (@pro\
+files, $profile_name);\n output_profile ($profil\
+e_name, \\%profile, $trim);\n print stdout \"\\t\
+Process: >$s{$seq}{name} _R_ $profile_name [$profi\
+le{n} Seq.] [$SERVER/blast/$db][$CACHE_STATUS]\\n\\
+";\n print R \">$s{$seq}{name} _R_ $profile_name\
+\\n\";\n }\n }\n close (R);\n &set_temporary_\
+dir (\"unset\",$mode, $method,\"result.aln\",$outf\
+ile, @profiles);\n}\nsub blast2pdb_template_test\n\
+ {\n my ($mode,$infile)=@_;\n my ($ma\
+xid,$minid,$mincov);\n $maxid=100;\n $mi\
+nid=0;\n $mincov=0;\n \n print \"$i\
+nfile\\n\";\n \n %p=blast_xml2profile($s\
+{$seq}{name}, $s{$seq}{seq},$maxid, $minid,$mincov\
+,$infile);\n $c=1;\n print stdout \"\\tP\
+rocess: >$s{$seq}{name} [$SERVER/blast/$db][$CACHE\
+_STATUS]\\n\";\n while (!$found && $c<$p{n})\\
+n {\n $pdbid=&id2pdbid($p{$c}{identifyer});\n \
+if ( length ($pdbid)>5){$pdbid=id2pdbid($p{$c}{def\
+inition});}\n \n if ( length ($pdbid)>5)\n \
+ {\n myexit(add_error (EXIT_FAILURE,$$,$$,ge\
+tppid(), \"BLAST_FAILURE::Could Not Parse PDBID ($\
+p{$c}{identifyer},$p{$c}{definition})\"));\n }\
+\n \n \n if (!&pdb_is_released($pdbid))\n \
+ {\n print stdout \"\\t\\t**$pdbid [PDB NOT\
+ RELEASED or WITHDRAWN]\\n\";\n $c++;\n \
+}\n elsif (!&pdb_has_right_type ($pdbid,$type))\\
+n {\n my $ptype=&pdb2type ($pdbid);\n \
+ my $etype=&type2etype($type);\n \n \
+ print stdout \"\\t\\t**$pdbid [$ptype cannot be u\
+sed (expected: $etype)]\\n\";\n $c++;\n \
+}\n else\n {\n $found=1;\n }\n }\n\
+\n if ($found)\n {\n print stdout \"\\t\\t \
+>$s{$seq}{name} _P_ $pdbid\\n\";\n }\n else\n\
+ {\n print stdout \"\\t\\t >$s{$seq}{name} No Te\
+mplate Selected\\n\";\n }\n die;\n }\nsub \
+blast2pdb_template \n {\n my ($mode, $infile, $d\
+b, $method, $outfile,$type)=@_;\n my %s, %h, ;\n \
+ my ($result,$blast_output);\n &set_temporary_dir\
+ (\"set\",$infile,\"seq.pep\");\n %s=read_fasta_s\
+eq (\"seq.pep\");\n open (R, \">result.aln\");\n \
+ \n \n #print stdout \"\\n\";\n foreach $seq (ke\
+ys(%s))\n {\n my $c;\n my $found;\n \
+ \n open (F, \">seqfile\");\n print (\
+F \">$A\\n$s{$seq}{seq}\\n\");\n close (F);\n\
+ \n $blast_output=&run_blast ($s{$seq}{na\
+me},$method, $db, \"seqfile\",\"outfile\");\n \
+\n %p=blast_xml2profile($s{$seq}{name}, $s{$s\
+eq}{seq},$maxid, $minid,$mincov,$blast_output);\n \
+ unlink ($blast_output);\n \n $c=1;\\
+n print stdout \"\\tProcess: >$s{$seq}{name} \
+[$SERVER/blast/$db][$CACHE_STATUS]\\n\";\n wh\
+ile (!$found && $c<$p{n})\n {\n $pdbid=&id2pdbid\
+($p{$c}{identifyer});\n if ( length ($pdbid)>5){\
+$pdbid=id2pdbid($p{$c}{definition});}\n\n if ( l\
+ength ($pdbid)>5)\n {\n myexit(add_error\
+ (EXIT_FAILURE,$$,$$,getppid(), \"BLAST_FAILURE::C\
+ould Not Parse PDBID ($p{$c}{identifyer},$p{$c}{de\
+finition})\"));\n }\n \n\n if (!&pdb_is_re\
+leased($pdbid))\n {\n print stdout \"\\t\
+\\t**$pdbid [PDB NOT RELEASED or WITHDRAWN]\\n\";\\
+n $c++;\n }\n elsif (!&pdb_has_right_t\
+ype ($pdbid,$type))\n {\n my $ptype=&pdb\
+2type ($pdbid);\n my $etype=&type2etype($typ\
+e);\n \n print stdout \"\\t\\t**$pdbid\
+ [$ptype cannot be used (expected: $etype)]\\n\";\\
+n $c++;\n }\n else\n {\n $fo\
+und=1;\n }\n }\n\n if ($found)\n {\n pr\
+int R \">$s{$seq}{name} _P_ $pdbid\\n\";\n print\
+ stdout \"\\t\\t >$s{$seq}{name} _P_ $pdbid\\n\";\\
+n }\n else\n {\n print R \">$s{$seq}{name}\\
+\n\";\n print stdout \"\\t\\t >$s{$seq}{name} No\
+ Template Selected\\n\";\n }\n }\n close (R);\\
+n &set_temporary_dir (\"unset\",$mode, $method,\"\
+result.aln\",$outfile);\n}\nsub type2etype\n {\n \
+ my $type=shift;\n my $etype;\n \n if (\
+ $type=~/n/){$etype.=\"NMR \";}\n if ( $type=~/\
+d/){$etype.=\"diffraction \";}\n if ( $type=~/m\
+/){$etype.=\"model \";}\n return $etype;\n }\n\
+sub pdb2type\n {\n my $pdb=shift;\n my $f\
+=vtmpnam();\n \n my $value= &safe_system (\
+\"t_coffee -other_pg extract_from_pdb -model_type \
+$pdb > $f\");\n my $r=&file2string ($f);\n \
+ chomp($r);\n return $r;\n }\nsub pdb_has_ri\
+ght_type\n {\n my $pdb=shift;\n my $type=sh\
+ift;\n \n my $f=vtmpnam();\n \n my $va\
+lue= &safe_system (\"t_coffee -other_pg extract_fr\
+om_pdb -model_type $pdb > $f\");\n my $r=&file2\
+string ($f);\n chomp($r);\n\n \n if (\
+ $r eq \"NMR\" && $type=~/n/){return 1;}\n elsi\
+f ( $r eq \"diffraction\" && $type=~/d/){return 1;\
+}\n elsif ( $r eq \"model\" && $type=~/m/){retu\
+rn 1;}\n else {return 0;}\n }\nsub pdb_is_rele\
+ased\n {\n my $pdb=shift;\n my $f=vtmpnam()\
+;\n \n $value= &safe_system (\"t_coffee -oth\
+er_pg extract_from_pdb -is_released_pdb_name $pdb \
+> $f\");\n my $r=&file2string ($f);\n chomp(\
+$r);\n return $r;\n }\nsub blast_msa\n {\n \
+ my ($infile,$db,$outfile)=@_;\n my ($a, %seq);\
+\n my $seqfile;\n my $SEQ=new FileHandle;\n \
+ my $seqfile=\"seqfile\";\n my @txt;\n \n \
+ \n %s1=&read_fasta_seq ($db);\n \n for\
+each $s (keys (%s1))\n {\n $i=$s1{$s}{order};\
+\n $s{$i}{name}=$s;\n $s{$i}{seq}=$s1{$s}{seq};\n \
+$s{$i}{len}=length( $s{$i}{seq});\n $s{n}++;\n \
+ }\n \n &safe_system (\"formatdb -i $db\");\
+\n &safe_system (\"blastall -i $infile -d $db \
+-m7 -p blastp -o io\");\n &set_blast_type (\"io\
+\");\n \n %FB=&xml2tag_list (\"io\", \"Itera\
+tion\");\n open (F, \">$outfile\");\n print \
+F \"! TC_LIB_FORMAT_01\\n\";\n print F \"$s{n}\\
+\n\";\n for ( $a=0; $a<$s{n}; $a++)\n {\n \
+print F \"$s{$a}{name} $s{$a}{len} $s{$a}{seq}\\n\\
+";\n }\n\n\n for ( $a=0; $a<$FB{n}; $a++)\\
+n {\n %p=blast_xml2profile ($s{$a}{name}, $s{\
+$a}{seq},100, 0, 0, $FB{$a}{body});\n my $query=$p\
+{0}{name};\n my $i= $s1{$query}{order}+1;\n for ($\
+b=1; $b<$p{n}; $b++)\n {\n my $l=length ($p{\
+$b}{Qseq});\n my $hit=$p{$b}{definition};\n \
+ my $Qstart=$p{$b}{Qstart};\n my $Hstart=$p{$\
+b}{Hstart};\n my $identity=$p{$b}{identity};\n\
+ my @lrQ=split (//,$p{$b}{Qseq});\n my @lr\
+H=split (//,$p{$b}{Hseq});\n \n my $j= $s1\
+{$hit}{order}+1;\n #if ( $j==$i){next;}\n \
+printf F \"# %d %d\\n\", $i, $j;\n # print F\
+ \"\\n$p{$b}{Qseq} ($Qstart)\\n$p{$b}{Hseq} ($Hsta\
+rt)\";\n for ($c=0; $c<$l; $c++)\n {\n \
+my $rQ=$lrQ[$c];\n my $rH=$lrH[$c];\n my $n=0;\n\
+ \n if ($rQ ne \"-\"){$n++, $Qstart++;}\n if ($\
+rH ne \"-\"){$n++; $Hstart++;}\n \n if ( $n==2)\\
+n {\n printf F \"\\t%d %d %d\\n\", $Qstart\
+-1, $Hstart-1,$identity;\n }\n }\n }\n \
+ }\n print F \"! SEQ_1_TO_N\\n\";\n clos\
+e (F);\n return $output;\n \n }\n\nsub blast_\
+msa_old\n {\n my ($infile,$outfile)=@_;\n m\
+y ($a, %seq);\n %s1=&read_fasta_seq ($infile);\\
+n foreach $s (keys (%s1))\n {\n $i=$s1{$s}\
+{order};\n $s{$i}{name}=$s;\n $s{$i}{seq}=$s1{$s}{\
+seq};\n $s{$i}{len}=length( $s{$i}{seq});\n $s{n}+\
++;\n }\n &safe_system (\"formatdb -i $infi\
+le\");\n &safe_system (\"blastall -i $infile -d\
+ $infile -m7 -o io\");\n &set_blast_type (\"io\\
+");\n \n %FB=&xml2tag_list (\"io\", \"Iterat\
+ion\");\n \n open (F, \">$outfile\");\n p\
+rint F \"! TC_LIB_FORMAT_01\\n\";\n print F \"$\
+s{n}\\n\";\n for ( $a=0; $a<$s{n}; $a++)\n \
+ {\n print F \"$s{$a}{name} $s{$a}{len} $s{$a}{seq\
+}\\n\";\n }\n for ( $a=0; $a<$FB{n}; $a++)\
+\n {\n %p=blast_xml2profile ($s{$a}{name}, $s\
+{$a}{seq},100, 0, 0, $FB{$a}{body});\n for ($b=1; \
+$b<$p{n}; $b++)\n {\n my $l=length ($p{$b}{Q\
+seq});\n my $hit=$p{$b}{definition};\n my \
+$Qstart=$p{$b}{Qstart};\n my $Hstart=$p{$b}{Hs\
+tart};\n my $identity=$p{$b}{identity};\n \
+my @lrQ=split (//,$p{$b}{Qseq});\n my @lrH=spl\
+it (//,$p{$b}{Hseq});\n my $i= $s1{$s{$a}{name\
+}}{order}+1;\n my $j= $s1{$hit}{order}+1;\n \
+ #if ( $j==$i){next;}\n printf F \"# %d %d\\n\
+\", $i, $j;\n # print F \"\\n$p{$b}{Qseq} ($\
+Qstart)\\n$p{$b}{Hseq} ($Hstart)\";\n for ($c=\
+0; $c<$l; $c++)\n {\n my $rQ=$lrQ[$c];\n m\
+y $rH=$lrH[$c];\n my $n=0;\n \n if ($rQ ne \"-\\
+"){$n++, $Qstart++;}\n if ($rH ne \"-\"){$n++; $H\
+start++;}\n \n if ( $n==2)\n {\n printf \
+F \"\\t%d %d %d\\n\", $Qstart-1, $Hstart-1,$identi\
+ty;\n }\n }\n }\n }\n print F \\
+"! SEQ_1_TO_N\\n\";\n close (F);\n return $o\
+utput;\n \n }\n\nsub seq2msa\n {\n my ($mode\
+, $infile, $method, $param, $outfile,$database)=@_\
+;\n &set_temporary_dir (\"set\",$infile,\"seq.p\
+ep\", $database, \"db.pep\");\n $param.=\" >/de\
+v/null 2>&1 \";\n \n \n #make sure test.p\
+ep is in FASTA\n &safe_system (\"t_coffee -othe\
+r_pg seq_reformat -in seq.pep -output fasta_seq > \
+x\");\n `mv x seq.pep`;\n \n if ( $method\
+ eq \"blastp\")\n {\n &blast_msa (\"seq.pep\"\
+, \"db.pep\",\"result.aln\");\n }\n elsif \
+( $method eq \"muscle\")\n {\n `muscle -in se\
+q.pep -out result.aln $param`;\n }\n elsif\
+ ( $method eq \"probcons\")\n {\n `probcons s\
+eq.pep >result.aln 2>/dev/null`;\n }\n els\
+if ( $method eq \"mafft\")\n {\n `mafft --qui\
+et --localpair --maxiterate 1000 seq.pep> result.a\
+ln 2>/dev/null`\n }\n elsif ( $method=~/p\
+rank/)\n {\n `$method -d=seq.pep -o=result.al\
+n -quiet 2>/dev/null`;\n `mv result.aln.1.fas resu\
+lt.aln`;\n }\n else\n {\n `$method -i\
+nfile=seq.pep -outfile=result.aln`;\n }\n \
+\n &set_temporary_dir (\"unset\",$mode, $method\
+,\"result.aln\",$outfile);\n myexit ($EXIT_SUCC\
+ESS);\n }\n\nsub seq2thread_pair\n {\n my ($m\
+ode, $infile, $pdbfile1, $method, $param, $outfile\
+)=@_;\n &set_temporary_dir (\"set\",$infile,\"s\
+eq.pep\",$pdbfile1,\"struc.pdb\");\n if ($metho\
+d eq \"fugueali\")\n {\n #Env Variable that n\
+eed to be defined for Fugue\n if (!$ENV{FUGUE_LIB_\
+LIST}){$ENV{FUGUE_LIB_LIST}=\"DUMMY\";}\n if (!$EN\
+V{HOMSTRAD_PATH}) {$ENV{HOMSTRAD_PATH}=\"DUMMY\";\
+}\n if (!$ENV{HOMS_PATH}){$ENV{HOMS_PATH}=\"DUMMY\\
+";}\n \n `joy struc.pdb >x 2>x`;\n &check_file(\"s\
+truc.tem\", \"Joy failed [FATAL:$PROGRAM/$method]\\
+");\n `melody -t struc.tem >x 2>x`;\n &check_file(\
+\"struc.tem\", \"Melody failed [FATAL:$PROGRAM/$me\
+thod]\");\n `fugueali -seq seq.pep -prf struc.fug \
+-print > tmp_result.aln`;\n \n &check_file(\"tmp_r\
+esult.aln\", \"Fugue failed [FATAL:$PROGRAM/$metho\
+d]\");\n &safe_system (\"t_coffee -other_pg seq_re\
+format -in tmp_result.aln -output fasta_aln >resul\
+t.aln\");\n }\n elsif ( $method eq \"t_cof\
+fee\")\n {\n &safe_system (\"t_coffee -in Pst\
+ruc.pdb Sseq.pep Mslow_pair -outfile result.aln -q\
+uiet\");\n }\n else\n {\n &safe_syste\
+m (\"$method -infile=seq.pep -pdbfile1=struc.pdb -\
+outfile=result.aln $param>x 2>x\");\n }\n \
+&set_temporary_dir (\"unset\",$mode,$method,\"resu\
+lt.aln\",$outfile);\n myexit ($EXIT_SUCCESS);\n\
+ }\nsub seq2pdbid_pair\n {\n my ($mode, $pdbf\
+ile1, $pdbfile2, $method, $param, $outfile)=@_;\n \
+ my ($name);\n\n \n &set_temporary_dir (\"\
+set\");\n $name=$pdbfile1.\" \".$pdbfile2;\n\n \
+ if ( &cache_file(\"GET\",\"\",\"$name\",\"$m\
+ethod\",\"dali\",$outfile,\"EBI\"))\n {return\
+ $outfile;}\n else\n {\n if ($method eq \"\
+daliweb\")\n {\n $pdbfile1=~/(....)(.)/;\n \
+ $id1=$1; $c1=$2;\n \n $pdbfile2=~/(....\
+)(.)/;\n $id2=$1; $c2=$2;\n \n $comman\
+d=\"t_coffee -other_pg dalilite.pl --pdb1 $id1 --c\
+hainid1 $c1 --pdb2 $id2 --chainid2 $c2 --email=$EM\
+AIL >dali_stderr 2>dali_stderr\";\n $dali=`$c\
+ommand`;\n \n open (F, \"dali_stderr\");\n\
+ while (<F>)\n {\n if ( /JobId: dalilit\
+e-(\\S+)/)\n {\n $jobid=$1;\n }\n }\n \
+ close (F);\n unlink (\"dali_stderr\");\n \
+ \n $output1=\"dalilite-$jobid.txt\";\n i\
+f ( -e $output1)\n {\n unlink ($output1);\n\
+ &url2file (\"http://www.ebi.ac.uk/Tools/es/cgi-b\
+in/jobresults.cgi/dalilite/dalilite-$jobid/aln.htm\
+l\", \"output2\");\n \n if ( -e \"output2\")\n \
+ {\n my ($seq1, $seq2);\n $seq1=$seq2=\\
+"\";\n \n open (F, \"output2\");\n \
+while (<F>)\n {\n $l=$_;\n if ( $l=~/Qu\
+ery\\s+(\\S+)/)\n {\n $seq1.=$1;\n }\
+\n elsif ( $l=~/Sbjct\\s+(\\S+)/)\n {\n \
+ $seq2.=$1;\n }\n }\n close (F);\\
+n unlink (\"output2\");\n if ($seq1 ne \\
+"\" && $seq2 ne \"\")\n {\n $output3=\">$\
+A\\n$seq1\\n>$B\\n$seq2\\n\";\n $output3=~s/\\./\
+-/g;\n open (F, \">result.aln\");\n print F \"\
+$output3\";\n close (F);\n }\n }\n \
+ }\n }\n }\n &cache_file(\"SET\",\"\",\
+\"$name\",\"$method\",\"dali\",\"result.aln\",\"EB\
+I\");\n &set_temporary_dir (\"unset\",$mode, $m\
+ethod, \"result.aln\",$outfile);\n myexit ($EXI\
+T_SUCCESS);\n }\nsub seq2pdb_pair\n {\n my ($\
+mode, $pdbfile1, $pdbfile2, $method, $param, $outf\
+ile)=@_;\n \n &set_temporary_dir (\"set\",$p\
+dbfile1,\"pdb1.pdb\",$pdbfile2,\"pdb2.pdb\");\n \
+ if ($method eq \"t_coffee\")\n {\n &safe_sys\
+tem (\"t_coffee -in Ppdb1.pdb Ppdb2.pdb -quiet -ou\
+tfile=result.aln\");\n }\n elsif ( $method\
+ eq \"DaliLite\")\n {\n if ( &safe_system (\"\
+DaliLite -pairwise pdb1.pdb pdb2.pdb >tmp1\")==$EX\
+IT_SUCCESS)\n {\n my ($seq1, $seq2);\n \
+ $seq1=$seq2=\"\";\n \n open (F, \"tmp1\\
+");\n while (<F>)\n {\n $l=$_;\n i\
+f ( $l=~/Query\\s+(\\S+)/)\n {\n $seq1.=\
+$1;\n }\n elsif ( $l=~/Sbjct\\s+(\\S+)/)\n \
+ {\n $seq2.=$1;\n }\n }\n \
+close (F);\n unlink (\"tmp1\");\n if ($s\
+eq1 ne \"\" && $seq2 ne \"\")\n {\n my $o\
+utput3=\">$A\\n$seq1\\n>$B\\n$seq2\\n\";\n $outp\
+ut3=~s/\\./-/g;\n open (F, \">result.aln\");\n \
+ print F \"$output3\";\n close (F);\n }\n\
+ }\n else\n {\n print \"ERROR: DalLite fa\
+iled to align the considered structures[tc_generic\
+_method.pl]\\n\";\n } \n }\n elsif ( \
+$method eq \"TMalign\")\n {\n if ( &safe_syst\
+em (\"TMalign pdb1.pdb pdb2.pdb >tmp1\")==$EXIT_SU\
+CCESS)\n {\n `tail -4 tmp1 > tmp2`;\n \n\
+ open (F, \"tmp2\");\n while (<F>)\n \
+ {\n unshift(@l, $_);\n }\n close (F);\\
+n open (F, \">result.aln\");\n $l[3]=~s/[^\
+a-zA-Z0-9-]/\\-/g;\n $l[1]=~s/[^a-zA-Z0-9-]/\\\
+-/g;\n print F \">$A\\n$l[3]\\n>$B\\n$l[1]\\n\\
+";\n close (F);\n }\n else\n {\n print\
+ \"ERROR: TMalign failed to align the considered s\
+tructures[tc_generic_method.pl]\\n\";\n `rm re\
+sult.aln >/dev/null 2>/dev/null`;\n }\n }\n\
+ elsif ( $method eq \"mustang\")\n {\n if \
+( &safe_system (\"mustang -i pdb1.pdb pdb2.pdb -F \
+fasta >/dev/null 2>/dev/null\")==$EXIT_SUCCESS)\n \
+ {\n `mv results.afasta result.aln`;\n }\n \
+else\n {\n print \"ERROR: mustang failed to \
+align the considered structures[tc_generic_method.\
+pl]\\n\";\n `rm result.aln >/dev/null 2>/dev/n\
+ull`;\n }\n }\n else\n {\n if ( &sa\
+fe_system (\"$method -pdbfile1=pdb1.pep -pdbfile2=\
+pdb2.pdb -outfile=result.aln $param>x 2>x\")==$EXI\
+T_SUCCESS)\n {\n `mv results.afasta result.a\
+ln`;\n }\n else\n {\n print \"ERROR: $meth\
+od failed to align the considered structures[tc_ge\
+neric_method.pl]\\n\";\n `rm result.aln >/dev/\
+null 2>/dev/null`;\n }\n }\n &set_tempor\
+ary_dir (\"unset\",$mode, $method, \"result.aln\",\
+$outfile);\n myexit ($EXIT_SUCCESS);\n }\n\nsu\
+b seq2profile_pair\n {\n my ($mode, $profile1,\
+ $profile2, $method, $param, $outfile)=@_;\n \n\
+ \n if ($method eq \"clustalw\")\n {\n \
+&set_temporary_dir (\"set\",$profile1,\"prf1.aln\"\
+,$profile2,\"prf2.aln\");\n `clustalw -profile1=pr\
+f1.aln -profile2=prf2.aln -outfile=result.aln`;\n \
+&set_temporary_dir (\"unset\",$mode, $method, \"re\
+sult.aln\",$outfile);\n }\n elsif ( $metho\
+d eq \"hhalign\")\n {\n hhalign ( $profile1,$\
+profile2,$outfile,$param);\n }\n else\n \
+ {\n \n `$method -profile1=prf1.aln -profile2=pr\
+f2.aln -outfile=result.aln $param>x 2>x`;\n }\
+\n \n myexit ($EXIT_SUCCESS);\n }\n\nsub pg_\
+is_installed\n {\n my @ml=@_;\n my ($r, $p,\
+ $m);\n my $supported=0;\n \n my $p=shift\
+ (@ml);\n if ($p=~/::/)\n {\n if (safe_sys\
+tem (\"perl -M$p -e 1\")==$EXIT_SUCCESS){return 1;\
+}\n else {return 0;}\n }\n else\n {\n\
+ $r=`which $p 2>/dev/null`;\n if ($r eq \"\"){$r=0\
+;}\n else {$r=1;}\n \n if ($r==0 && is_blast_packa\
+ge ($p)){return pg_is_installed (\"legacy_blast.pl\
+\");}\n else {return $r;}\n }\n }\n\nsub is_\
+blast_package\n {\n my $p=shift;\n if ( $p=\
+~/blastp/){return 1;}\n elsif ($p=~/blastall/){\
+return 1;}\n elsif ($p=~/blastn/){return 1;}\n \
+ elsif ($p=~/blastx/){return 1;}\n elsif ($p=\
+~/formatdb/){return 1;}\n else {return 0;}\n }\
+\n \nsub check_internet_connection\n {\n my\
+ $internet;\n my $tmp;\n &check_configuratio\
+n ( \"wget\"); \n \n $tmp=&vtmpnam ();\n \
+\n if (&pg_is_installed (\"wget\")){`wge\
+t www.google.com -O$tmp >/dev/null 2>/dev/null`;}\\
+n elsif (&pg_is_installed (\"curl\")){`curl\
+ www.google.com -o$tmp >/dev/null 2>/dev/null`;}\n\
+ \n if ( !-e $tmp || -s $tmp < 10){$internet\
+=0;}\n else {$internet=1;}\n if (-e $tmp){un\
+link $tmp;}\n\n return $internet;\n }\nsub che\
+ck_pg_is_installed\n {\n my @ml=@_;\n my $r\
+=&pg_is_installed (@ml);\n if (!$r && $p=~/::/)\
+\n {\n print STDERR \"\\nYou Must Install the\
+ perl package $p on your system.\\nRUN:\\n\\tsudo \
+perl -MCPAN -e 'install $pg'\\n\";\n }\n e\
+lsif (!$r)\n {\n myexit(flush_error(\"\\nProg\
+ram $p Supported but Not Installed on your system\\
+"));\n }\n else\n {\n return 1;\n \
+ }\n }\nsub set_temporary_dir\n {\n my @list\
+=@_;\n my $dir_mode, $a, $mode, $method;\n \n \
+ $dir_mode=shift (@list);\n\n \n if ( $dir\
+_mode eq \"set\")\n {\n $initial_dir=cwd();\n\
+ if ( !$tmp_dir)\n {\n $rand=rand (100000);\\
+n $tmp_dir=\"$TMPDIR/tmp4tcoffee_profile_pair_\
+dir_$$\\_P_$rand\";\n }\n if ( !-d $tmp_dir)\n \
+ {\n push (@TMPDIR_LIST, $tmp_dir);\n `mkd\
+ir $tmp_dir`;\n }\n \n for ( $a=0; $a<=$#list; $\
+a+=2)\n {\n if (-e $list[$a]){ `cp $list[$a\
+] $tmp_dir/$list[$a+1]`;}\n }\n chdir $tmp_d\
+ir;\n }\n elsif ( $dir_mode eq \"unset\")\\
+n {\n $mode=shift (@list);\n $method=shift (@\
+list);\n \n if (!-e $list[0])\n {\n myexit(fl\
+ush_error(\"Program $method failed to produce $lis\
+t[1]\" ));\n myexit ($EXIT_FAILURE);\n }\n e\
+lse\n {\n chdir $initial_dir;\n # `t_cof\
+fee -other_pg seq_reformat -in $tmp_dir/$list[0] -\
+output fasta_aln -out $tmp_dir/result2.aln`;\n \
+ `cp $tmp_dir/$list[0] $tmp_dir/result2.aln`;\n \
+ if ( $list[1] eq \"stdout\")\n {\n open (\
+F, \"$tmp_dir/result2.aln\");\n while (<F>){print\
+ $_;}close(F);\n }\n else\n {\n `\
+mv $tmp_dir/result2.aln $list[1]`;\n }\n \
+ shift (@list); shift (@list);\n foreach $f (@\
+list)\n {\n if (-e (\"$tmp_dir/$f\")){`mv $\
+tmp_dir/$f .`;}\n }\n }\n }\n }\n\n\\
+n\n\nsub my_get_opt\n {\n my @list=@_;\n my\
+ $cl, $a, $argv, @argl;\n \n @argl=();\n \
+$cl=shift @list;\n for ( $a=0; $a<=$#list; $a+=\
+3)\n {\n $option=$list[$a];\n $optional=$list\
+[$a+1];\n $status=$list[$a+2];\n $argv=\"\";\n if \
+($cl=~/$option(\\S+)/){$argv=$1;}\n @argl=(@argl,$\
+argv);\n \n \n #$optional:0=>optional\n #$optional\
+:1=>must be set\n #$status: 0=>no requirement\n #$\
+status: 1=>must be an existing file\n #$status: 2=\
+>must be an installed package\n \n\n if ($optional\
+==0){;}\n elsif ( $optional==1 && $argv eq \"\")\n\
+ {\n myexit(flush_error( \"ERROR: Option $op\
+tion must be set\"));\n myexit ($EXIT_FAILURE)\
+;\n }\n if ($status==0){;}\n elsif ($status ==1 \
+&& $argv ne \"\" && !-e $argv)\n {\n myexit(\
+flush_error( \"File $argv must exist\"));\n my\
+exit ($EXIT_FAILURE);\n }\n elsif ( $status==2 &\
+& $argv ne \"\" && &check_pg_is_installed ($argv)=\
+=0)\n {\n myexit(flush_error( \" $argv is no\
+t installed\"));\n myexit ($EXIT_FAILURE);\n \
+ }\n }\n\n return @argl;\n }\n\nsub che\
+ck_file \n {\n my ($file, $msg)=@_;\n\n if \
+( !-e $file)\n {\n myexit(flush_error(\"$msg\\
+"));\n }\n }\nsub hhalign\n {\n my ($a\
+ln1, $aln2, $outfile, $param)=@_;\n my $h1, $h2\
+;\n \n $h{0}{index}=0;\n $h{1}{index}=1;\\
+n \n $h{0}{aln}=$aln1;\n $h{1}{aln}=$aln2\
+;\n\n \n\n %{$h{0}}=aln2psi_profile (%{$h{0}}\
+);\n %{$h{1}}=aln2psi_profile (%{$h{1}});\n\n \
+ $param=~s/#S/ /g;\n $param=~s/#M/\\-/g;\n \
+$param=~s/#E/\\=/g;\n \n\n \n $command=\"\
+hhalign -i $h{0}{a3m} -t $h{1}{a3m} -tc $outfile.t\
+mp -rank 1 -mapt 0 $param\";\n `$command`;\n \
+ \n # `hhalign -i $h{0}{a3m} -t $h{1}{a3m} -tc $\
+outfile.tmp -rank 1 -mapt 0 -gapf 0.8 -gapg 0.8`;\\
+n \n\n # To run global use the following\n \
+ \n open (I, \"$outfile.tmp\");\n open (O, \
+\">$outfile\");\n $h{0}{cons}=s/\\./x/g;\n $\
+h{1}{cons}=s/\\./x/g;\n\n print O \"! TC_LIB_FO\
+RMAT_01\\n2\\n$h{0}{name} $h{0}{len} $h{0}{seq}\\n\
+$h{1}{name} $h{1}{len} $h{1}{seq}\\n#1 2\\n\";\n \
+ \n while (<I>)\n {\n if (/(\\d+)\\s+(\\d\
++)\\s+(\\d+)/)\n {\n print O \"\\t$h{0}{$1}\\
+\t$h{1}{$2}\\t$3\\n\";\n }\n }\n print O\
+ \"! SEQ_1_TO_N\\n\";\n\n close (O);\n close\
+ (I);\n }\n\nsub aln2psi_profile\n {\n my (%h\
+)=@_;\n my ($aln,$i,$hv, $a, @c, $n);\n \n \
+ $i=$h{index};\n $aln=$h{aln};\n\n `cp $aln \
+$$.hhh_aln`;\n $command=\"t_coffee -other_pg se\
+q_reformat -in $aln -output hasch\";\n $hv=`$co\
+mmand`;chomp ($hv);\n \n $h{a2m}=\"$tmp/$hv.\
+tmp4hhpred.a2m\";\n $h{a3m}=\"$tmp/$hv.tmp4hhpr\
+ed.a3m\";\n if ( -e $h{a3m}){;}\n else\n \
+ {\n `hhconsensus -M 50 -i $h{aln} -oa2m $h{a2m}\
+`;\n if (!-e $h{a2m})\n {\n print STDERR \"P\
+rogram tc_generic_method.pl FAILED to run:\\n\\thh\
+consensus -M 50 -i $h{aln} -oa2m $h{a2m}\";\n \
+ myexit ($EXIT_FAILURE);\n }\n \n `hhconsensus \
+-M 50 -i $h{aln} -oa3m $h{a3m}`;\n if (!-e $h{a3m}\
+)\n {\n print STDERR \"Program tc_generic_me\
+thod.pl FAILED to run:\\n\\thhconsensus -M 50 -i \
+$h{aln} -oa3m $h{a3m}\";\n myexit ($EXIT_FAILU\
+RE);\n }\n `buildali.pl $h{a3m} -n 1`;\n \
+ }\n \n \n $h{a2m_seq}=`head -n 2 $h{a\
+2m} | grep -v \">\"`;chomp ($h{a2m_seq});\n $h{\
+a3m_seq}=`head -n 2 $h{a3m} | grep -v \">\"`;chomp\
+ ($h{a3m_seq});\n $h{cons}=$h{a2m_seq};\n $h\
+{seq}=`head -n 2 $h{aln} | grep -v \">\"`;chomp ($\
+h{seq});\n \n \n\n @c=split (//, $h{cons}\
+);\n $h{len}=$#c+1;\n for ($n=0,$a=0, $b=0; \
+$a<$h{len};$a++)\n {\n if ( $c[$a]=~/[A-Z]/)\\
+n {\n $h{++$n}=++$b;\n\n }\n elsif ( $c[$a\
+]=~/[a-z\\.]/)\n {\n ++$b;\n }\n }\n \
+ \n $name=`head -n 2 $h{aln} | grep \">\"`;\n\
+ $name=~/\\>(\\S+)/;\n $h{name}=$1;\n \n \
+ `cp $h{a2m} $i.a2m`;\n `cp $h{a3m} $i.a3m`;\\
+n `cp $h{aln} $i.hh_aln`;\n \n return %h;\
+\n }\n\nsub read_fasta_seq \n {\n my $f=@_[0]\
+;\n my %hseq;\n my (@seq, @com, @name);\n \
+ my ($a, $s,$nseq);\n\n open (F, $f);\n whil\
+e (<F>)\n {\n $s.=$_;\n }\n close (F)\
+;\n\n \n @name=($s=~/>(\\S*).*\\n[^>]*/g);\n\
+ \n @seq =($s=~/>.*.*\\n([^>]*)/g);\n @co\
+m =($s=~/>\\S*(.*)\\n([^>]*)/g);\n\n \n $nse\
+q=$#name+1;\n \n for ($a=0; $a<$nseq; $a++)\\
+n {\n my $s;\n my $n=$name[$a];\n $hseq{$n}{n\
+ame}=$n;\n $seq[$a]=~s/[^A-Za-z]//g;\n $hseq{$n}{o\
+rder}=$a;\n $hseq{$n}{seq}=$seq[$a];\n $hseq{$n}{c\
+om}=$com[$a];\n \n }\n return %hseq;\n }\\
+n\nsub file_contains \n {\n my ($file, $tag, $\
+max)=(@_);\n my ($n);\n $n=0;\n \n if \
+( !-e $file && ($file =~/$tag/)) {return 1;}\n \
+elsif ( !-e $file){return 0;}\n else \n {\\
+n open (FC, \"$file\");\n while ( <FC>)\n {\n \
+ if ( ($_=~/$tag/))\n {\n close (FC);\n r\
+eturn 1;\n }\n elsif ($max && $n>$max)\n\
+ {\n close (FC);\n return 0;\n }\n \
+ $n++;\n }\n }\n close (FC);\n retu\
+rn 0;\n }\n \n \nsub file2string\n {\n \
+my $f=@_[0];\n my $string, $l;\n open (F,\"$\
+f\");\n while (<F>)\n {\n\n $l=$_;\n #chom\
+p ($l);\n $string.=$l;\n }\n close (F);\n \
+ $string=~s/\\r\\n//g;\n $string=~s/\\n//g;\n\
+ return $string;\n }\n\n\nsub my_get_opt\n {\\
+n my @list=@_;\n my $cl, $a, $argv, @argl;\n\
+ \n @argl=();\n $cl=shift @list;\n for\
+ ( $a=0; $a<=$#list; $a+=3)\n {\n $option=$li\
+st[$a];\n $optional=$list[$a+1];\n $status=$list[$\
+a+2];\n $argv=\"\";\n if ($cl=~/$option(\\S+)/){$a\
+rgv=$1;}\n @argl=(@argl,$argv);\n \n \n #$optional\
+:0=>optional\n #$optional:1=>must be set\n #$statu\
+s: 0=>no requirement\n #$status: 1=>must be an exi\
+sting file\n #$status: 2=>must be an installed pac\
+kage\n \n\n if ($optional==0){;}\n elsif ( $option\
+al==1 && $argv eq \"\")\n {\n\n myexit(flush\
+_error(\"Option $option must be set\"));\n \n \
+ }\n if ($status==0){;}\n elsif ($status ==1 && $a\
+rgv ne \"\" && !-e $argv)\n {\n myexit(flus\
+h_error(\"File $argv must exist\"));\n \n }\n\
+ elsif ( $status==2 && $argv ne \"\" && &check_pg_\
+is_installed ($argv)==0)\n {\n myexit(flush_\
+error(\"$argv is not installed\"));\n \n }\n \
+ }\n\n return @argl;\n }\n\nsub tag2valu\
+e \n {\n \n my $tag=(@_[0]);\n my $word=\
+(@_[1]);\n my $return;\n \n $tag=~/$word=\
+\"([^\"]+)\"/;\n $return=$1;\n return $retur\
+n;\n }\n \nsub hit_tag2pdbid\n {\n my $t\
+ag=(@_[0]);\n my $pdbid;\n \n $tag=~/i\
+d=\"(\\S+)\"/;\n $pdbid=$1;\n $pdbid=~s/_//;\
+\n return $pdbid;\n }\nsub id2pdbid\n {\n \
+my $in=@_[0];\n my $id;\n \n $in=~/(\\S+)\
+/;\n $id=$in;\n $id=~s/PDB/pdb/g;\n \n \
+ if ($id =~/pdb(.*)/){$id=$1;}\n elsif ( $id=~/\
+(\\S+)\\s+mol:protein/){$id=$1;}\n $id=~s/[:|ï¿\
+½ï¿½_]//g;\n return $id;\n }\nsub set_blast_ty\
+pe \n {\n my $file =@_[0];\n if (&file_cont\
+ains ($file,\"EBIApplicationResult\",100)){$BLAST_\
+TYPE=\"EBI\";}\n elsif (&file_contains ($file,\\
+"NCBI_BlastOutput\",100)) {$BLAST_TYPE=\"NCBI\";}\\
+n else\n {\n $BLAST_TYPE=\"\";\n }\n \
+ return $BLAST_TYPE;\n }\nsub is_valid_blast_xm\
+l\n {\n my $file=shift;\n my $line;\n\
+ \n \n if ( !-e $file) {return 0;}\\
+n $line=&file2tail ($file,100);\n if ( $\
+line=~/<\\/EBIApplicationResult/ || $line=~/<\\/NC\
+BI_BlastOutput/ || $line=~/<\\/BlastOutput/ ){retu\
+rn 1;}\n return 0;\n }\nsub file2blast_fla\
+vor\n {\n my $file=shift;\n if (&file_contain\
+s ($file,\"EBIApplicationResult\",100)){return \"E\
+BI\";}\n elsif (&file_contains ($file,\"NCBI_Blast\
+Output\",100)){return \"NCBI\";}\n else {return \"\
+UNKNOWN\";}\n }\nsub blast_xml2profile \n {\\
+n my ($name,$seq,$maxid, $minid, $mincov, $file\
+)=(@_);\n my (%p, $a, $string, $n);\n \n \
+\n\n if ($BLAST_TYPE eq \"EBI\" || &file_contai\
+ns ($file,\"EBIApplicationResult\",100)){%p=ebi_bl\
+ast_xml2profile(@_);}\n elsif ($BLAST_TYPE eq \\
+"NCBI\" || &file_contains ($file,\"NCBI_BlastOutpu\
+t\",100)){%p=ncbi_blast_xml2profile(@_);}\n els\
+e \n {\n myexit(add_error ( $$,$$,getppid(), \
+\"BLAST_FAILURE::unkown XML\",$CL));\n }\n \
+ for ($a=0; $a<$p{n}; $a++)\n {\n my $name=$p\
+{$a}{name};\n $p{$name}{seq}=$p{$a}{seq};\n $p{$na\
+me}{index}=$a;\n }\n return %p;\n }\nsub \
+ncbi_tblastx_xml2lib_file \n {\n my ($outlib,\
+$string)=(@_);\n my ($L,$l, $a,$b,$c,$d,$i,$nhi\
+ts,@identifyerL);\n my (%ITERATION);\n \n \
+ open (F, \">>$outlib\");\n \n $seq=~s/[^a\
+-zA-Z]//g;\n $L=length ($seq);\n \n %ITER\
+ATION=xml2tag_list ($string, \"Iteration\");\n \
+for ($i=0; $i<$ITERATION{n};$i++)\n {\n my ($\
+qindex, $qlen, %hit, $string);\n $string=$ITERATIO\
+N{$i}{body};\n\n $qindex=xmltag2value($string,\"It\
+eration_iter-num\");\n $qlen =xmltag2value($strin\
+g,\"Iteration_query-len\");\n %hit=&xml2tag_list \
+($string, \"Hit\");\n\n for ($a=0; $a<$hit{n}; $a+\
++)\n {\n my ($string);\n $string=$hit{$a\
+}{body};\n \n $hindex=xmltag2value($string,\"\
+Hit_accession\")+1;\n if ($hindex<=$qindex){ne\
+xt;}\n else {print F \"# $qindex $hindex\\n\\
+";}\n \n \n $hlen=xmltag2value ($strin\
+g,\"Hit_len\");\n %HSP=&xml2tag_list ($string\
+, \"Hsp\");\n \n for ($b=0; $b<$HSP{n}; $b+\
++)\n {\n my ($string, $qs,$qe,$qf,$hs,$he,$\
+hf,$s, $d, $e);\n $string=$HSP{$b}{body};\n \n $\
+qs=xmltag2value ($string,\"Hsp_query-from\");\n \
+$qe=xmltag2value ($string,\"Hsp_query-to\");\n $\
+qf=xmltag2value ($string,\"Hsp_query-frame\");\n\\
+n $hs=xmltag2value ($string,\"Hsp_hit-from\");\n\
+ $he=xmltag2value ($string,\"Hsp_hit-to\");\n $\
+hf=xmltag2value ($string,\"Hsp_hit-frame\");\n \\
+n $s=xmltag2value ($string,\"Hsp_identity\");\n \
+ $l=xmltag2value ($string,\"Hsp_align-len\");\n \
+$s=int(($s*100)/$l);\n \n if ($qf>0)\n {$rqs=\
+$qs; $rqe=$qe;}\n else\n {\n $rqe=($qlen-\
+$qs)+1;\n $rqs=($qlen-$qe)+1;\n }\n \n i\
+f ($hf>0)\n {$rhs=$hs; $rhe=$he;}\n else\n \
+{\n $rhe=($hlen-$hs)+1;\n $rhs=($hlen-$h\
+e)+1;\n }\n for ($d=0,$e=$rqs; $e<$rqe; $e++,$\
+d++)\n {\n my ($r1,$r2);\n $r1=$e;\n \
+ $r2=$rhs+$d;\n print F \" $r1 $r2 $s 0\\\
+n\";\n }\n }\n }\n }\n print F \
+\"! SEQ_1_TO_N\\n\";\n \n close (F);\n re\
+turn %lib;\n }\n\nsub ncbi_tblastpx_xml2lib_file \
+\n {\n my ($outlib,$string,%s)=(@_);\n my \
+($L,$l, $a,$b,$c,$d,$i,$nhits,@identifyerL);\n \
+my (%ITERATION,%hdes, %qdes);\n \n open (F\
+, \">>$outlib\");\n \n $seq=~s/[^a-zA-Z]//g;\
+\n $L=length ($seq);\n \n %ITERATION=xml2\
+tag_list ($string, \"Iteration\");\n for ($i=0;\
+ $i<$ITERATION{n};$i++)\n {\n my ($qindex, $q\
+len, %hit, $string);\n $string=$ITERATION{$i}{body\
+};\n\n $qdef=xmltag2value($string,\"Iteration_quer\
+y-def\");\n %qdes=&tblastpx_name2description($qdef\
+,%s);\n $qlen =xmltag2value($string,\"Iteration_q\
+uery-len\");\n %hit=&xml2tag_list ($string, \"Hit\
+\");\n\n for ($a=0; $a<$hit{n}; $a++)\n {\n \
+my ($string);\n $string=$hit{$a}{body};\n \
+$hdef=xmltag2value($string,\"Hit_def\");\n %hd\
+es=&tblastpx_name2description($hdef,%s);\n if \
+($hdes{index}<=$qdes{index}){next;}\n else {p\
+rint F \"# $qdes{index} $hdes{index}\\n\";}\n \
+ \n \n $hlen=xmltag2value ($string,\"Hit_l\
+en\");\n %HSP=&xml2tag_list ($string, \"Hsp\"\
+);\n \n for ($b=0; $b<$HSP{n}; $b++)\n \
+ {\n my ($string, $l,$qs,$qe,$qf,$hs,$he,$hf,$s,\
+ $d, $e, @s1, @s2);\n $string=$HSP{$b}{body};\n \\
+n $qs=xmltag2value ($string,\"Hsp_query-from\");\
+\n $qe=xmltag2value ($string,\"Hsp_query-to\");\\
+n $qf=$qdes{frame};\n $qseq=xmltag2value ($stri\
+ng,\"Hsp_qseq\");\n \n $hs=xmltag2value ($strin\
+g,\"Hsp_hit-from\");\n $he=xmltag2value ($string\
+,\"Hsp_hit-to\");\n $hf=$hdes{frame};\n $hseq=xm\
+ltag2value ($string,\"Hsp_hseq\");\n \n $s=xmlt\
+ag2value ($string,\"Hsp_identity\");\n $l=xmltag\
+2value ($string,\"Hsp_align-len\");\n $s=int(($s\
+*100)/$l);\n @s1=tblastpx_hsp2coordinates($qseq,$\
+qs,$qe,%qdes);\n @s2=tblastpx_hsp2coordinates($hs\
+eq,$hs,$he,%hdes);\n \n \n for ($f=0; $f<=$#s1;\
+ $f++)\n {\n if ($s1[$f]==-1 || $s2[$f]==-\
+1){next;}\n else \n {\n print F \" $\
+s1[$f] $s2[$f] $s 0\\n\";\n }\n }\n \
+ }\n }\n }\n print F \"! SEQ_1_TO_N\\n\\
+";\n \n close (F);\n return %lib;\n }\ns\
+ub tblastpx_hsp2coordinates\n {\n my ($seq, $s\
+, $e, %des)=@_;\n my @list;\n my @sa;\n m\
+y @gap=(-1,-1,-1);\n \n $s=$des{start}+3*($s\
+-1);\n \n if ($des{strand} eq \"d\"){;}\n e\
+lse {$s=($des{length}-$s)+1;}\n \n foreach $\
+c (split (//,$seq))\n {\n if ( $c eq '-'){pus\
+h (@list,@gap);}\n elsif ($des{strand} eq \"d\")\n\
+ {\n push(@list,$s++,$s++,$s++);\n }\n els\
+e\n {\n push(@list, $s--,$s--,$s--);\n }\n\
+ }\n return @list;\n }\n\nsub tblastpx_na\
+me2description\n {\n my ($name, %s)=@_;\n m\
+y @at=split(\"__\", $name);\n my %des;\n\n $\
+des{name}=$at[0];\n $des{strand}=$at[1];\n \\
+n $des{start}=$at[2];\n $des{end}=$at[3];\n \
+ $des{length}=$at[4];\n $des{index}=$s{$at[0]\
+}{order}+1;\n return %des;\n } \nsub ncbi_bla\
+st_xml2profile \n {\n my ($name,$seq,$maxid, $\
+minid, $mincov, $string)=(@_);\n my ($L,$l, $a,\
+$b,$c,$d,$nhits,@identifyerL);\n \n \n $s\
+eq=~s/[^a-zA-Z]//g;\n $L=length ($seq);\n \n \
+ #This is causing the NCBI parser to fail when I\
+teration_query-def is missing \n #%query=&xml2t\
+ag_list ($string, \"Iteration_query-def\");\n #\
+$name=$query{0}{body};\n \n %hit=&xml2tag_li\
+st ($string, \"Hit\");\n \n \n for ($nhit\
+s=0,$a=0; $a<$hit{n}; $a++)\n {\n my ($ldb,$i\
+d, $identity, $expectation, $start, $end, $coverag\
+e, $r);\n my (%ID,%DE,%HSP);\n \n $ldb=\"\";\n\n %\
+ID=&xml2tag_list ($hit{$a}{body}, \"Hit_id\");\n $\
+identifyer=$ID{0}{body};\n \n %DE=&xml2tag_list ($\
+hit{$a}{body}, \"Hit_def\");\n $definition=$DE{0}{\
+body};\n \n %HSP=&xml2tag_list ($hit{$a}{body}, \"\
+Hsp\");\n for ($b=0; $b<$HSP{n}; $b++)\n {\n \
+ my (%START,%END,%E,%I,%Q,%M);\n\n \n %START=\
+&xml2tag_list ($HSP{$b}{body}, \"Hsp_query-from\")\
+;\n %HSTART=&xml2tag_list ($HSP{$b}{body}, \"H\
+sp_hit-from\");\n \n %LEN= &xml2tag_list \
+($HSP{$b}{body}, \"Hsp_align-len\");\n %END= \
+&xml2tag_list ($HSP{$b}{body}, \"Hsp_query-to\");\\
+n %HEND= &xml2tag_list ($HSP{$b}{body}, \"Hsp\
+_hit-to\");\n %E=&xml2tag_list ($HSP{$b}{b\
+ody}, \"Hsp_evalue\");\n %I=&xml2tag_list \
+($HSP{$b}{body}, \"Hsp_identity\");\n %Q=&xml2\
+tag_list ($HSP{$b}{body}, \"Hsp_qseq\");\n \
+ %M=&xml2tag_list ($HSP{$b}{body}, \"Hsp_hseq\\
+");\n \n for ($e=0; $e<$Q{n}; $e++)\n\n \
+ {\n $qs=$Q{$e}{body};\n $ms=$M{$e}{body};\n \
+ \n $expectation=$E{$e}{body};\n $identity=($LEN\
+{$e}{body}==0)?0:$I{$e}{body}/$LEN{$e}{body}*100;\\
+n $start=$START{$e}{body};\n $end=$END{$e}{body}\
+;\n $Hstart=$HSTART{$e}{body};\n $Hend=$HEND{$e}\
+{body};\n \n $coverage=($L)?(($end-$start)*100)/$\
+L:0;\n \n if ($identity>$maxid || $identity<$mini\
+d || $coverage<$mincov){next;}\n @lr1=(split (//,\
+$qs));\n @lr2=(split (//,$ms));\n $l=$#lr1+1;\n \
+ for ($c=0;$c<$L;$c++){$p[$nhits][$c]=\"-\";}\n f\
+or ($d=0,$c=0; $c<$l; $c++)\n {\n $r=$lr1[\
+$c];\n if ( $r=~/[A-Za-z]/)\n {\n \n\
+ $p[$nhits][$d + $start-1]=$lr2[$c];\n $d++;\n\
+ }\n }\n $Qseq[$nhits]=$qs;\n $Hseq[$n\
+hits]=$ms;\n $QstartL[$nhits]=$start;\n $HstartL\
+[$nhits]=$Hstart;\n $identityL[$nhits]=$identity;\
+\n $endL[$nhits]=$end;\n $definitionL[$nhits]=$d\
+efinition;\n $identifyerL[$nhits]=$identifyer;\n \
+ $comment[$nhits]=\"$ldb|$identifyer [Eval=$expect\
+ation][id=$identity%][start=$Hstart end=$Hend]\";\\
+n $nhits++;\n }\n }\n }\n \n \\
+n $profile{n}=0;\n $profile{$profile{n}}{nam\
+e}=$name;\n $profile{$profile{n}}{seq}=$seq;\n \
+ $profile {n}++;\n \n for ($a=0; $a<$nhits\
+; $a++)\n {\n $n=$a+1;\n \n $profile{$n}{name\
+}=\"$name\\_$a\";\n $profile{$n}{seq}=\"\";\n $pro\
+file{$n}{Qseq}=$Qseq[$a];\n $profile{$n}{Hseq}=$Hs\
+eq[$a];\n $profile{$n}{Qstart}=$QstartL[$a];\n $pr\
+ofile{$n}{Hstart}=$HstartL[$a];\n $profile{$n}{ide\
+ntity}=$identityL[$a];\n $profile{$n}{definition}=\
+$definitionL[$a];\n $profile{$n}{identifyer}=$iden\
+tifyerL[$a];\n $profile{$n}{comment}=$comment[$a];\
+\n\n for ($b=0; $b<$L; $b++)\n {\n if ($p[$a\
+][$b])\n {\n $profile{$n}{seq}.=$p[$a][$b];\
+\n }\n else\n {\n $profile{$n}{se\
+q}.=\"-\";\n }\n }\n }\n \n $pr\
+ofile{n}=$nhits+1;\n return %profile;\n }\nsub\
+ ebi_blast_xml2profile \n {\n my ($name,$seq,$\
+maxid, $minid, $mincov, $string)=(@_);\n my ($L\
+,$l, $a,$b,$c,$d,$nhits,@identifyerL,$identifyer);\
+\n \n\n \n $seq=~s/[^a-zA-Z]//g;\n $L=\
+length ($seq);\n %hit=&xml2tag_list ($string, \\
+"hit\");\n \n for ($nhits=0,$a=0; $a<$hit{n}\
+; $a++)\n {\n my ($ldb,$id, $identity, $expec\
+tation, $start, $end, $coverage, $r);\n my (%Q,%M,\
+%E,%I);\n \n $ldb=&tag2value ($hit{$a}{open}, \"da\
+tabase\");\n $identifyer=&tag2value ($hit{$a}{open\
+}, \"id\");\n\n $description=&tag2value ($hit{$a}{\
+open}, \"description\");\n \n %Q=&xml2tag_list ($h\
+it{$a}{body}, \"querySeq\");\n %M=&xml2tag_list ($\
+hit{$a}{body}, \"matchSeq\");\n %E=&xml2tag_list (\
+$hit{$a}{body}, \"expectation\");\n %I=&xml2tag_li\
+st ($hit{$a}{body}, \"identity\");\n \n\n for ($b=\
+0; $b<$Q{n}; $b++)\n {\n\n $qs=$Q{$b}{body};\
+\n $ms=$M{$b}{body};\n \n $expectation\
+=$E{$b}{body};\n $identity=$I{$b}{body};\n \
+ \n \n $start=&tag2value ($Q{$b}{open\
+}, \"start\");\n $end=&tag2value ($Q{$b}{open}\
+, \"end\");\n $startM=&tag2value ($M{$b}{open}\
+, \"start\");\n $endM=&tag2value ($M{$b}{open}\
+, \"end\");\n $coverage=(($end-$start)*100)/$L\
+;\n \n # print \"$id: ID: $identity COV: $c\
+overage [$start $end]\\n\";\n \n if ($iden\
+tity>$maxid || $identity<$minid || $coverage<$minc\
+ov){next;}\n # print \"KEEP\\n\";\n\n \n \
+ @lr1=(split (//,$qs));\n @lr2=(split (//,$m\
+s));\n $l=$#lr1+1;\n for ($c=0;$c<$L;$c++)\
+{$p[$nhits][$c]=\"-\";}\n for ($d=0,$c=0; $c<$\
+l; $c++)\n {\n $r=$lr1[$c];\n if ( $r=~/[A\
+-Za-z]/)\n {\n \n $p[$nhits][$d + $st\
+art-1]=$lr2[$c];\n $d++;\n }\n }\n \
+ \n $Qseq[$nhits]=$qs;\n $Hseq[$nhits]=$ms\
+;\n $QstartL[$nhits]=$start;\n $HstartL[$n\
+hits]=$Hstart;\n $identityL[$nhits]=$identity;\
+\n $endL[$nhits]=$end;\n $definitionL[$nhi\
+ts]=$definition;\n $identifyerL[$nhits]=$ident\
+ifyer;\n $comment[$nhits]=\"$ldb|$identifyer [\
+Eval=$expectation][id=$identity%][start=$startM en\
+d=$endM]\";\n $nhits++;\n }\n }\n \n\
+ $profile{n}=0;\n $profile{$profile{n}}{name\
+}=$name;\n $profile{$profile{n}}{seq}=$seq;\n \
+ $profile {n}++;\n \n for ($a=0; $a<$nhits;\
+ $a++)\n {\n $n=$a+1;\n $profile{$n}{name}=\"\
+$name\\_$a\";\n $profile{$n}{seq}=\"\";\n $profile\
+{$n}{Qseq}=$Qseq[$a];\n $profile{$n}{Hseq}=$Hseq[$\
+a];\n $profile{$n}{Qstart}=$QstartL[$a];\n $profil\
+e{$n}{Hstart}=$HstartL[$a];\n $profile{$n}{identit\
+y}=$identityL[$a];\n $profile{$n}{definition}=$def\
+initionL[$a]; \n $profile{$n}{identifyer}=$identif\
+yerL[$a];\n $profile{$n}{comment}=$comment[$a];\n\\
+n for ($b=0; $b<$L; $b++)\n {\n if ($p[$a][$\
+b])\n {\n $profile{$n}{seq}.=$p[$a][$b];\n \
+ }\n else\n {\n $profile{$n}{seq}.\
+=\"-\";\n }\n }\n }\n $profile{n}=\
+$nhits+1;\n \n return %profile;\n }\nsub ou\
+tput_profile\n {\n my ($outfile,$profileR, $tr\
+im)=(@_);\n my ($a);\n my %profile=%$profile\
+R;\n my $P= new FileHandle;\n my $tmp=vtmpna\
+m();\n \n open ($P, \">$tmp\");\n for ($a\
+=0; $a<$profile{n}; $a++)\n {\n print $P \">$\
+profile{$a}{name} $profile{$a}{comment}\\n$profile\
+{$a}{seq}\\n\";\n }\n close ($P);\n\n i\
+f ( $trim)\n {\n &safe_system (\"t_coffee -ot\
+her_pg seq_reformat -in $tmp -action +trim _aln_%%\
+$trim\\_K1 -output fasta_aln -out $outfile\");\n \
+ }\n else\n {\n &safe_system (\"mv $tmp\
+ $outfile\");\n }\n return;\n }\nsub blas\
+t_xml2hit_list\n {\n my $string=(@_[0]);\n \
+return &xml2tag_list ($string, \"hit\");\n }\nsub\
+ xmltag2value\n {\n my ($string_in, $tag)=@_;\\
+n my %TAG;\n %TAG=xml2tag_list ($string_in, \
+$tag);\n return $TAG{0}{body};\n }\n \nsu\
+b xml2tag_list \n {\n my ($string_in,$tag)=@_\
+;\n my $tag_in, $tag_out;\n my %tag;\n \n\
+ if (-e $string_in)\n {\n $string=&file2st\
+ring ($string_in);\n }\n else\n {\n $\
+string=$string_in;\n }\n $tag_in1=\"<$tag \
+\";\n $tag_in2=\"<$tag>\";\n $tag_out=\"/$ta\
+g>\";\n $string=~s/>/>##1/g;\n $string=~s/</\
+##2</g;\n $string=~s/##1/<#/g;\n $string=~s/\
+##2/#>/g;\n @l=($string=~/(\\<[^>]+\\>)/g);\n \
+ $tag{n}=0;\n $in=0;$n=-1;\n \n \n\n forea\
+ch $t (@l)\n {\n\n $t=~s/<#//;\n $t=~s/#>//;\\
+n \n if ( $t=~/$tag_in1/ || $t=~/$tag_in2/)\n {\\
+n \n $in=1;\n $tag{$tag{n}}{open}=$t;\n \
+ $n++;\n \n }\n elsif ($t=~/$tag_out/)\n \
+ {\n \n\n $tag{$tag{n}}{close}=$t;\n $\
+tag{n}++;\n $in=0;\n }\n elsif ($in)\n {\n\
+ \n $tag{$tag{n}}{body}.=$t;\n }\n }\
+\n \n return %tag;\n }\n\n\nsub seq2gor_predi\
+ction \n {\n my ($name, $seq,$infile, $outfile\
+, $gor_seq, $gor_obs)=(@_);\n my ($l);\n \n \
+ `gorIV -prd $infile -seq $gor_seq -obs $gor_obs\
+ > gor_tmp`;\n open (GR, \">$outfile\");\n o\
+pen (OG, \"gor_tmp\");\n\n while (<OG>)\n \
+{\n \n $l=$_;\n if ($l=~/\\>/){print GR \"$l\";}\n\
+ elsif ( $l=~/Predicted Sec. Struct./)\n {\n \
+ $l=~s/Predicted Sec. Struct\\.//;\n print GR \
+\"$l\";\n }\n }\n close (GR);\n close\
+ (OG);\n return;\n }\nsub seq2msa_tm_predictio\
+n \n {\n my ($name, $seq, $db, $infile, $outfi\
+le, $arch, $psv)=(@_);\n my (%p,%gseq,%R, $blas\
+t_output, %s, $l);\n my $R2=new FileHandle;\n \
+ my $db=\"uniprot\";\n my $method=\"psitm\";\n\
+ my $SERVER=\"EBI\";\n \n $blast_output=&\
+run_blast ($name,\"blastp\", $db, $infile, \"outfi\
+le\");\n \n if (&cache_file(\"GET\",$infile,\
+$name,$method,$db,$outfile,$SERVER))\n {\n pr\
+int \"\\tPSITM: USE Cache\\n\";\n return $outfile;\
+\n }\n else\n {\n $CACHE_STATUS=\"COM\
+PUTE CACHE\";\n %p=blast_xml2profile($name,$seq,$m\
+axid, $minid,$mincov,$blast_output);\n \n \n open \
+(F, \">tm_input\");\n for (my $a=0; $a<$p{n}; $a++\
+)\n {\n my $s;\n \n $s=$p{$a}{seq};\\
+n $s=uc($s);\n print F \">$p{$a}{name}\\n$\
+s\\n\";\n #print stdout \">$p{$a}{name}\\n$s\\\
+n\";\n }\n close (F);\n print \"\\tPSITM: kept \
+$p{n} Homologues for Sequence $p{0}{name}\\n\";\n \
+&safe_system (\"t_coffee -other_pg fasta_seq2hmmto\
+p_fasta.pl -in=tm_input -out=$outfile -output=cons\
+ -cov=70 -trim=95 -arch=$arch -psv=$psv\");\n unli\
+nk (\"tm_input\");\n &cache_file(\"SET\",$infile,$\
+name,$method,$db,$outfile,$SERVER);\n return;\n \
+ }\n }\n\n\nsub seq2msa_gor_prediction \n {\n \
+ my ($name, $seq,$infile, $outfile, $gor_seq, $g\
+or_obs)=(@_);\n my (%p,%gseq,%R, $blast_output,\
+ %s, $l);\n my $R2=new FileHandle;\n my $db=\
+\"uniprot\";\n my $method=\"psigor\";\n my $\
+SERVER=\"EBI\";\n \n $blast_output=&run_blas\
+t ($name,\"blastp\", \"uniprot\", $infile, \"outfi\
+le\");\n \n if (&cache_file(\"GET\",$infile,\
+$name,$method,$db,$outfile,$SERVER))\n {\n pr\
+int \"\\tPSIGOR: USE Cache\\n\";\n return $outfile\
+;\n }\n else\n {\n $CACHE_STATUS=\"CO\
+MPUTE CACHE\";\n %p=blast_xml2profile($name,$seq,$\
+maxid, $minid,$mincov,$blast_output);\n \n \n open\
+ (F, \">gor_input\");\n for (my $a=0; $a<$p{n}; $a\
+++)\n {\n my $s;\n \n $s=$p{$a}{seq}\
+;\n $s=uc($s);\n print F \">$p{$a}{name}\\\
+n$s\\n\";\n #print stdout \">$p{$a}{name}\\n$s\
+\\n\";\n }\n close (F);\n print \"\\tGORTM: kept\
+ $p{n} Homologues for Sequence $p{0}{name}\\n\";\\
+n &safe_system (\"t_coffee -other_pg fasta_seq2hmm\
+top_fasta.pl -in=gor_input -out=$outfile -output=c\
+ons -cov=70 -trim=95 -gor_seq=$gor_seq -gor_obs=$g\
+or_obs -mode=gor\");\n unlink (\"tm_input\");\n &c\
+ache_file(\"SET\",$infile,$name,$method,$db,$outfi\
+le,$SERVER);\n return;\n }\n }\n\n\n\nsub ru\
+n_blast\n {\n my ($name, $method, $db, $infile\
+, $outfile, $run)=(@_);\n if (!$run){$run=1;}\n\
+ \n \n if (&cache_file(\"GET\",$infile,$n\
+ame,$method,$db,$outfile,$SERVER) && is_valid_blas\
+t_xml ($outfile))\n {return $outfile;}\n e\
+lse\n {\n $CACHE_STATUS=\"COMPUTE CACHE\";\n \
+if ( $SERVER eq \"EBI_SOAP\")\n {\n &check_c\
+onfiguration (\"EMAIL\",\"SOAP::Light\",\"INTERNET\
+\");\n \n $cl_method=$method;\n if ($c\
+l_method =~/wu/)\n {\n $cl_method=~s/wu//;\\
+n if ( $cl_method eq \"psiblast\")\n {\n \
+add_warning($$,$$,\"PSI BLAST cannot be used with \
+the wuBLAST Client. Use server=EBI Or server=LOCAL\
+. blastp will be used instead\");\n $cl_metho\
+d=\"blastp\";\n }\n \n $command=\"t_coffee -o\
+ther_pg wublast.pl --email $EMAIL $infile -D $db -\
+p $cl_method --outfile $outfile -o xml>/dev/null 2\
+>/dev/null\";\n &safe_system ( $command);\n if (\
+-e \"$outfile.xml\") {`mv $outfile.xml $outfile`;}\
+\n }\n else\n {\n if ($cl_method \
+eq \"psiblast\"){$cl_method =\"blastp -j5\";}\n \\
+n $command=\"t_coffee -other_pg blastpgp.pl --ema\
+il $EMAIL $infile -d $db --outfile $outfile -p $cl\
+_method --mode PSI-Blast>/dev/null 2>/dev/null\";\\
+n &safe_system ( $command);\n \n if (-e \"$outf\
+ile.xml\") {`mv $outfile.xml $outfile`;}\n }\
+\n }\n elsif ($SERVER eq \"EBI_REST\" || $SERVER\
+ eq \"EBI\")\n {\n \n $cl_method=$method;\
+\n &check_configuration(\"EMAIL\",\"XML::Simpl\
+e\", \"INTERNET\");\n if ($db eq \"uniprot\"){\
+$db1=\"uniprotkb\";}\n else {$db1=$db;}\n \
+\n\n if ($cl_method =~/wu/)\n {\n $cl_m\
+ethod=~s/wu//;\n if ( $cl_method eq \"psiblast\")\
+{$cl_method=\"blastp\";}\n \n $command=\"t_coffe\
+e -other_pg wublast_lwp.pl --email $EMAIL -D $db1 \
+-p $cl_method --outfile $outfile --align 7 --stype\
+ protein $infile>/dev/null 2>/dev/null\";\n \n \
+ }\n else\n {\n if ( $cl_method =~/p\
+siblast/){$cl_method =\"blastp -j5\";}\n $command\
+=\"t_coffee -other_pg ncbiblast_lwp.pl --email $EM\
+AIL -D $db1 -p $cl_method --outfile $outfile --ali\
+gn 7 --stype protein $infile>/dev/null 2>/dev/null\
+\";\n }\n &safe_system ( $command,5);\n \
+ if (-e \"$outfile.out.xml\") {`mv $outfile.out\
+.xml $outfile`;}\n elsif (-e \"$outfile.xml.xm\
+l\"){`mv $outfile.xml.xml $outfile`;}\n elsif \
+(-e \"$outfile.out..xml\") {`mv $outfile.out..xml \
+$outfile`;}\n elsif (-e \"$outfile.xml..xml\")\
+{`mv $outfile.xml..xml $outfile`;}\n }\n elsif (\
+$SERVER eq \"NCBI\")\n {\n &check_configurat\
+ion (\"blastcl3\",\"INTERNET\");\n if ($db eq \
+\"uniprot\"){$cl_db=\"nr\";}\n else {$cl_db=$d\
+b;}\n \n if ( $method eq \"psiblast\")\n \
+ {\n add_warning($$,$$,\"PSI BLAST cannot be \
+used with the NCBI BLAST Client. Use server=EBI Or\
+ server=LOCAL. blastp will be used instead\");\n \
+$cl_method=\"blastp\";\n }\n else\n \
+ {\n $cl_method=$method;\n }\n $comman\
+d=\"blastcl3 -p $cl_method -d $cl_db -i $infile -o\
+ $outfile -m 7\";\n &safe_system ($command);\n\
+ }\n elsif ($SERVER =~/CLIENT_(.*)/)\n {\n \
+ my $client=$1;\n $command=\"$client -p $metho\
+d -d $db -i $infile -o $outfile -m 7\";\n &saf\
+e_system ($command);\n }\n elsif ( $SERVER eq \"\
+LOCAL_blastall\")\n {\n &check_configuration\
+ (\"blastall\");\n if ($method eq \"blastp\")\\
+n {\n $command=\"blastall -d $db -i $infile\
+ -o $outfile -m7 -p blastp\";\n }\n &saf\
+e_system ($command);\n }\n elsif ( $SERVER eq \"\
+LOCAL\")\n {\n \n if ($ENV{\"BLAST_DB_DI\
+R\"})\n {\n $x=$ENV{\"BLAST_DB_DIR\"};\n $\
+cl_db=\"$x$db\";\n }\n else\n {\n \
+ $cl_db=$db;\n }\n \n if ($method eq\
+ \"blastp\")\n {\n &check_configuration(\"b\
+lastpgp\");\n $command=\"blastpgp -d $cl_db -i $i\
+nfile -o $outfile -m7 -j1\";\n }\n elsif\
+ ($method eq \"psiblast\")\n {\n &check_con\
+figuration(\"blastpgp\");\n $command=\"blastpgp -\
+d $cl_db -i $infile -o $outfile -m7 -j5\";\n \
+ }\n elsif ($method eq \"blastn\")\n {\n\
+ &check_configuration(\"blastall\");\n $command=\
+\"blastall -p blastn -d $cl_db -i $infile -o $outf\
+ile -m7 -W6\";\n } \n &safe_system ($com\
+mand);\n }\n else\n {\n \n myexit(add_\
+error (EXIT_FAILURE,$$,$$,getppid(), \"BLAST_FAILU\
+RE::UnknownServer\",$CL));\n }\n \n if ( !-e $ou\
+tfile || !&is_valid_blast_xml($outfile))\n {\n \
+ \n if ( -e $outfile)\n {\n add_warni\
+ng ($$,$$,\"Corrupted Blast Output (Run $run)\");\\
+n unlink($outfile);\n }\n \n if ( $\
+run==$BLAST_MAX_NRUNS)\n {\n \n myexit(add_\
+error (EXIT_FAILURE,$$,$$,getppid(), \"BLAST_FAILU\
+RE::UnknownReason\", \"$command\"));\n }\n \
+ else\n {\n my $out;\n if ($SERVER eq \"\
+NCBI\") {$SERVER=\"EBI\"; }\n elsif ($SERVER eq \\
+"EBI\"){$SERVER=\"NCBI\";}\n add_warning ($$,$$,\\
+"Blast for $name failed (Run: $run out of $BLAST_M\
+AX_NRUNS. Use $SERVER)\");\n $out=&run_blast ($na\
+me, $method, $db,$infile, $outfile, $run+1);\n if\
+ ($SERVER eq \"NCBI\") {$SERVER=\"EBI\"; }\n elsi\
+f ($SERVER eq \"EBI\"){$SERVER=\"NCBI\";}\n retur\
+n $out;\n }\n }\n \n &cache_file(\"SET\",$\
+infile,$name,$method,$db,$outfile,$SERVER);\n #sys\
+tem (\"cp $outfile ~/Dropbox/tmp/cedric.out\");\n \
+#die;\n return $outfile;\n }\n }\n\nsub cach\
+e_file\n {\n my ($cache_mode,$infile,$name,$me\
+thod,$db, $outfile,$server)=(@_);\n my $cache_f\
+ile;\n #Protect names so that they can be turne\
+d into legal filenames\n $name=&clean_file_name\
+ ($name);\n\n if ($db=~/\\//)\n {\n $db=~/\
+([^\\/]+)$/;\n $db=$1;\n }\n $cache_file_s\
+h=\"$name.$method.$db.$server.tmp\";\n $cache_f\
+ile=\"$CACHE/$name.$method.$db.$server.tmp\";\n \
+ \n if ($infile ne \"\")\n {\n $cache_file\
+_infile_sh=\"$name.$method.$db.$server.infile.tmp\\
+";\n $cache_file_infile=\"$CACHE/$name.$method.$db\
+.$server.infile.tmp\";\n }\n \n if ($ca\
+che_mode eq \"GET\")\n {\n if ($CACHE eq \"\"\
+ || $CACHE eq \"no\" || $CACHE eq \"ignore\" || $\
+CACHE eq \"local\" || $CACHE eq \"update\"){return\
+ 0;}\n elsif ( !-d $CACHE)\n {\n print STDER\
+R \"ERROR: Cache Dir: $CACHE Does not Exist\";\n \
+ return 0;\n }\n else\n {\n if ( -e $cac\
+he_file && &fasta_file1_eq_fasta_file2($infile,$ca\
+che_file_infile)==1)\n {\n `cp $cache_file \
+$outfile`;\n $CACHE_STATUS=\"READ CACHE\";\n ret\
+urn 1;\n }\n }\n }\n elsif ($cache\
+_mode eq \"SET\")\n {\n if ($CACHE eq \"\" ||\
+ $CACHE eq \"no\" || $CACHE eq \"ignore\" || $CAC\
+HE eq \"local\" || $CACHE eq \"update\"){return 0;\
+}\n elsif ( !-d $CACHE)\n {\n print STDERR \\
+"ERROR: Cache Dir: $CACHE Does not Exist\";\n \
+return 0;\n }\n elsif (-e $outfile)\n {\n \
+`cp $outfile $cache_file`;\n if ($cache_file_i\
+nfile ne \"\"){ `cp $infile $cache_file_infile`;}\\
+n\n #functions for updating the cache\n #`\
+t_coffee -other_pg clean_cache.pl -file $cache_fil\
+e_sh -dir $CACHE`;\n #`t_coffee -other_pg clea\
+n_cache.pl -file $cache_file_infile_sh -dir $CACHE\
+`;\n return 1;\n }\n }\n $CACHE_STAT\
+US=\"COMPUTE CACHE\";\n return 0;\n }\nsub fil\
+e1_eq_file2\n {\n my ($f1, $f2)=@_;\n if ( \
+$f1 eq \"\"){return 1;}\n elsif ( $f2 eq \"\"){\
+return 1;}\n elsif ( !-e $f1){return 0;}\n e\
+lsif ( !-e $f2){return 0;}\n elsif ($f1 eq \"\"\
+ || $f2 eq \"\" || `diff $f1 $f2` eq \"\"){return \
+1;}\n \n return 0;\n }\nsub clean_file_name\
+ \n {\n my $name=@_[0];\n \n $name=~s/[^\
+A-Za-z1-9.-]/_/g;\n return $name;\n }\nsub url\
+2file\n {\n my ($address, $out)=(@_);\n \n \
+ if (&pg_is_installed (\"wget\"))\n {\n return\
+ &safe_system (\"wget $address -O$out >/dev/null 2\
+>/dev/null\");\n }\n elsif (&pg_is_installed (\\
+"curl\"))\n {\n return &safe_system (\"curl $\
+address -o$out >/dev/null 2>/dev/null\");\n }\
+\n else\n {\n myexit(flus_error(\"neither \
+curl nor wget are installed. Imnpossible to fectch\
+ remote file\"));\n exit ($EXIT_FAILURE);\n }\
+\n }\nsub fasta_file1_eq_fasta_file2\n {\n my\
+ ($f1, $f2)=@_;\n my (%s1, %s2);\n my @names\
+;\n %s1=read_fasta_seq ($f1);\n %s2=read_fas\
+ta_seq ($f2);\n\n @names=(keys (%s1));\n \n \
+ foreach $n (keys(%s1))\n {\n if ($s1{$n}{s\
+eq} ne $s2{$n}{seq}){return 0;}\n } \n \n \
+ foreach $n (keys(%s2))\n {\n if ($s1{$n}{s\
+eq} ne $s2{$n}{seq}){return 0;}\n }\n retu\
+rn 1;\n }\n \n\n\nsub read_template_file\n{\n my \
+$pdb_templates = @_[0];\n open (TEMP, \"<$pdb_temp\
+lates\");\n my %temp_h;\n while (<TEMP>)\n{\n $li\
+ne = $_;\n $line =~/(\\S+)\\s(\\S+)/;\n $temp_\
+h{$1}= $2;\n}\n close(TEMP);\n return %temp_h;\n}\\
+n\nsub calc_rna_template\n{\n my ($mode, $infile, \
+$pdbfile, $outfile)=@_;\n my %s, %h ;\n my $result\
+;\n my (@profiles);\n &set_temporary_dir (\"set\",\
+$infile,\"seq.pep\");\n %s=read_fasta_seq (\"seq.p\
+ep\");\n \n %pdb_template_h = &read_template_file(\
+$pdbfile);\n my $pdb_chain;\n open (R, \">result.a\
+ln\");\n\n\n #print stdout \"\\n\";\n foreach $seq\
+ (keys(%s))\n {\n if ($pdb_template_h{$seq} eq \"\
+\")\n {\n next;\n }\n open (F, \">seqfile\");\
+\n print (F \">$s{$seq}{name}\\n$s{$seq}{seq}\\n\\
+");\n close (F);\n $pdb_chain = $pdb_template_h{\
+$seq};\n $lib_name=\"$s{$seq}{name}.rfold\";\n $\
+lib_name=&clean_file_name ($lib_name);\n \n saf\
+e_system (\"secondary_struc.py seqfile $CACHE$pdb_\
+chain $lib_name\");\n \n if ( !-e $lib_name)\n \
+ {\n myexit(flush_error(\"RNAplfold failed to com\
+pute the secondary structure of $s{$seq}{name}\"))\
+;\n myexit ($EXIT_FAILURE);\n }\n else\n {\n \
+ print stdout \"\\tProcess: >$s{$seq}{name} _F_ $\
+lib_name\\n\";\n print R \">$s{$seq}{name} _F_ $\
+lib_name\\n\";\n }\n unshift (@profiles, $lib_na\
+me);\n }\n close (R);\n &set_temporary_dir (\"unse\
+t\",$mode, $method,\"result.aln\",$outfile, @profi\
+les);\n}\n\n\n\nsub seq2rna_pair{\n my ($mode, $pd\
+bfile1, $pdbfile2, $method, $param, $outfile)=@_;\\
+n \n if ($method eq \"runsara.py\")\n {\n open(TM\
+P,\"<$pdbfile1\");\n my $count = 0;\n my $line;\\
+n while (<TMP>)\n {\n $line = $_;\n if ($cou\
+nt ==1)\n {\n last;\n }\n $count += 1;\n \
+ }\n\n \n $chain1 = substr($line,length($line)-3\
+,1);\n\n close TMP;\n open(TMP,\"<$pdbfile2\");\\
+n my $count = 0;\n while (<TMP>)\n {\n $line \
+= $_;\n if ($count ==1)\n {\n last;\n }\n\
+ $count += 1;\n }\n $chain2 = substr($line,len\
+gth($line)-3,1);\n close TMP;\n\n $tmp_file=&vtm\
+pnam();\n \n safe_system(\"runsara.py $pdbfile1 $\
+chain1 $pdbfile2 $chain2 -s -o $tmp_file --limitat\
+ion 5000 > /dev/null 2> /dev/null\") == 0 or die \\
+"sara did not work $!\\n\";\n open(TMP,\"<$tmp_fi\
+le\") or die \"cannot open the sara tmp file:$!\\n\
+\";\n open(OUT,\">$outfile\") or die \"cannot ope\
+n the $outfile file:$!\\n\";\n\n my $switch = 0;\\
+n my $seqNum = 0;\n foreach my $line (<TMP>)\n \
+{\n next unless ($line=~/SARAALI/);\n if ($lin\
+e=~/>/)\n {\n $switch =0;\n print OUT \">s\
+eq$seqNum\\n\";\n $seqNum++; \n }\n if (\
+$switch < 2){\n $switch++;\n next;\n }\n \\
+n if ($line =~/REMARK\\s+SARAALI\\s+([^\\*]+)\\*\
+/)\n {\n my $string = $1;\n print OUT \"$s\
+tring\\n\";\n }\n }\n close TMP; \n close OUT\
+;\n unlink($tmp_file);\n }\n}\n\nsub seq2tblastx_\
+lib\n {\n my ($mode, $infile, $outfile)=@_;\n \
+ my (%s, $method,$nseq);\n\n $method=$mode;\n\
+ &set_temporary_dir (\"set\",$infile,\"infile\"\
+);\n %s=read_fasta_seq(\"infile\");\n \n \
+\n foreach $seq (keys(%s))\n {\n $slist[$s\
+{$seq}{order}]=$s{$seq}{seq};\n $sname[$s{$seq}{or\
+der}]=$s{$seq}{name};\n $slen[$s{$seq}{order}]=len\
+gth ($s{$seq}{seq});\n }\n $nseq=$#sname+1\
+;\n open (F, \">outfile\");\n print F \"! TC\
+_LIB_FORMAT_01\\n\";\n print F \"$nseq\\n\";\n \
+ for ($a=0; $a<$nseq;$a++)\n {\n print F \"\
+$sname[$a] $slen[$a] $slist[$a]\\n\"\n }\n \
+ close (F);\n &safe_system (\"formatdb -i infi\
+le -p F\");\n &safe_system (\"blastall -p tblas\
+tx -i infile -d infile -m 7 -S1>blast.output\");\n\
+ \n ncbi_tblastx_xml2lib_file (\"outfile\", \
+file2string (\"blast.output\"));\n &set_tempora\
+ry_dir (\"unset\",$mode, $method, \"outfile\",$out\
+file);\n myexit ($EXIT_SUCCESS);\n }\nsub se\
+q2tblastpx_lib\n {\n my ($mode, $infile, $outf\
+ile)=@_;\n my (%s, $method,$nseq);\n $method\
+=$mode;\n &set_temporary_dir (\"set\",$infile,\\
+"infile\");\n %s=read_fasta_seq(\"infile\");\n \
+ \n foreach $seq (keys(%s))\n {\n $slist\
+[$s{$seq}{order}]=$s{$seq}{seq};\n $sname[$s{$seq}\
+{order}]=$s{$seq}{name};\n $slen[$s{$seq}{order}]=\
+length ($s{$seq}{seq});\n }\n $nseq=$#snam\
+e+1;\n open (F, \">outfile\");\n print F \"!\
+ TC_LIB_FORMAT_01\\n\";\n print F \"$nseq\\n\";\
+\n for ($a=0; $a<$nseq;$a++)\n {\n print F\
+ \"$sname[$a] $slen[$a] $slist[$a]\\n\"\n }\\
+n close (F);\n &safe_system(\"t_coffee -othe\
+r_pg seq_reformat -in infile -output tblastx_db1 >\
+ tblastxdb\");\n &safe_system (\"formatdb -i tb\
+lastxdb -p T\");\n &safe_system (\"blastall -p \
+blastp -i tblastxdb -d tblastxdb -m7 >blast.output\
+\");\n ncbi_tblastpx_xml2lib_file (\"outfile\",\
+ file2string (\"blast.output\"), %s);\n &set_te\
+mporary_dir (\"unset\",$mode, $method, \"outfile\"\
+,$outfile);\n myexit ($EXIT_SUCCESS);\n }\n\\
+n\n \n\n\n\nsub file2head\n {\n my $file =\
+ shift;\n my $size = shift;\n my $f= new FileHandl\
+e;\n my $line;\n open ($f,$file);\n read ($f,$line\
+, $size);\n close ($f);\n return $line;\n }\n\
+sub file2tail\n {\n my $file = shift;\n my $s\
+ize = shift;\n my $f= new FileHandle;\n my $line;\\
+n \n open ($f,$file);\n seek ($f,$size*-1, 2);\n r\
+ead ($f,$line, $size);\n close ($f);\n return $lin\
+e;\n }\n\n\nsub vtmpnam\n {\n my $r=rand\
+(100000);\n my $f=\"file.$r.$$\";\n while (-e $f)\\
+n {\n $f=vtmpnam();\n }\n push (@TMPFILE_L\
+IST, $f);\n return $f;\n }\n\nsub myexit\n {\
+\n my $code=@_[0];\n if ($CLEAN_EXIT_STARTED\
+==1){return;}\n else {$CLEAN_EXIT_STARTED=1;}\n\
+ ### ONLY BARE EXIT\n exit ($code);\n }\nsu\
+b set_error_lock\n {\n my $name = shift;\n\
+ my $pid=$$;\n\n \n &lock4tc ($$,\"\
+LERROR\", \"LSET\", \"$$ -- ERROR: $name $PROGRAM\\
+\n\");\n return;\n }\nsub set_lock\n {\n \
+ my $pid=shift;\n my $msg= shift;\n my $p=\
+getppid();\n &lock4tc ($pid,\"LLOCK\",\"LRESET\\
+",\"$p$msg\\n\");\n }\nsub unset_lock\n {\n \
+ \n my $pid=shift;\n &lock4tc ($pid,\"LLOCK\\
+",\"LRELEASE\",\"\");\n }\nsub shift_lock\n {\n \
+ my $from=shift;\n my $to=shift;\n my $fro\
+m_type=shift;\n my $to_type=shift;\n my $act\
+ion=shift;\n my $msg;\n \n if (!&lock4tc(\
+$from, $from_type, \"LCHECK\", \"\")){return 0;}\n\
+ $msg=&lock4tc ($from, $from_type, \"LREAD\", \\
+"\");\n &lock4tc ($from, $from_type,\"LRELEASE\\
+", $msg);\n &lock4tc ($to, $to_type, $action, $\
+msg);\n return;\n }\nsub isshellpid\n {\n \
+my $p=shift;\n if (!lock4tc ($p, \"LLOCK\", \"L\
+CHECK\")){return 0;}\n else\n {\n my $c=lo\
+ck4tc($p, \"LLOCK\", \"LREAD\");\n if ( $c=~/-SHEL\
+L-/){return 1;}\n }\n return 0;\n }\nsub \
+isrootpid\n {\n if(lock4tc (getppid(), \"LLOCK\
+\", \"LCHECK\")){return 0;}\n else {return 1;}\\
+n }\nsub lock4tc\n {\n my ($pid,$type,$action,$\
+value)=@_;\n my $fname;\n my $host=hostname;\n\
+ \n if ($type eq \"LLOCK\"){$fname=\"$LOCKDIR/\
+.$pid.$host.lock4tcoffee\";}\n elsif ( $type eq \
+\"LERROR\"){ $fname=\"$LOCKDIR/.$pid.$host.error4t\
+coffee\";}\n elsif ( $type eq \"LWARNING\"){ $fn\
+ame=\"$LOCKDIR/.$pid.$host.warning4tcoffee\";}\n \
+ \n if ($debug_lock)\n {\n print STDER\
+R \"\\n\\t---lock4tc(tcg): $action => $fname =>$va\
+lue (RD: $LOCKDIR)\\n\";\n }\n\n if ($act\
+ion eq \"LCHECK\") {return -e $fname;}\n elsif (\
+$action eq \"LREAD\"){return file2string($fname);}\
+\n elsif ($action eq \"LSET\") {return string2fi\
+le ($value, $fname, \">>\");}\n elsif ($action e\
+q \"LRESET\") {return string2file ($value, $fname,\
+ \">\");}\n elsif ($action eq \"LRELEASE\") \n \
+ {\n if ( $debug_lock)\n {\n my $g=new\
+ FileHandle;\n open ($g, \">>$fname\");\n pr\
+int $g \"\\nDestroyed by $$\\n\";\n close ($g);\
+\n safe_system (\"mv $fname $fname.old\");\n }\
+\n else\n {\n unlink ($fname);\n }\n \
+ }\n return \"\";\n }\n \nsub file2string\n {\n\
+ my $file=@_[0];\n my $f=new FileHandle;\n m\
+y $r;\n open ($f, \"$file\");\n while (<$f>){$\
+r.=$_;}\n close ($f);\n return $r;\n }\nsub st\
+ring2file \n {\n my ($s,$file,$mode)=@_;\n \
+ my $f=new FileHandle;\n \n open ($f, \"$mo\
+de$file\");\n print $f \"$s\";\n close ($f)\
+;\n }\n\nBEGIN\n {\n srand;\n \n \
+$SIG{'SIGUP'}='signal_cleanup';\n $SIG{'SIGIN\
+T'}='signal_cleanup';\n $SIG{'SIGQUIT'}='sign\
+al_cleanup';\n $SIG{'SIGILL'}='signal_cleanup\
+';\n $SIG{'SIGTRAP'}='signal_cleanup';\n \
+ $SIG{'SIGABRT'}='signal_cleanup';\n $SIG{'SI\
+GEMT'}='signal_cleanup';\n $SIG{'SIGFPE'}='si\
+gnal_cleanup';\n \n $SIG{'SIGKILL'}='sig\
+nal_cleanup';\n $SIG{'SIGPIPE'}='signal_clean\
+up';\n $SIG{'SIGSTOP'}='signal_cleanup';\n \
+ $SIG{'SIGTTIN'}='signal_cleanup';\n $SIG{'\
+SIGXFSZ'}='signal_cleanup';\n $SIG{'SIGINFO'}\
+='signal_cleanup';\n \n $SIG{'SIGBUS'}='\
+signal_cleanup';\n $SIG{'SIGALRM'}='signal_cl\
+eanup';\n $SIG{'SIGTSTP'}='signal_cleanup';\n\
+ $SIG{'SIGTTOU'}='signal_cleanup';\n $SI\
+G{'SIGVTALRM'}='signal_cleanup';\n $SIG{'SIGU\
+SR1'}='signal_cleanup';\n\n\n $SIG{'SIGSEGV'}\
+='signal_cleanup';\n $SIG{'SIGTERM'}='signal_\
+cleanup';\n $SIG{'SIGCONT'}='signal_cleanup';\
+\n $SIG{'SIGIO'}='signal_cleanup';\n $SI\
+G{'SIGPROF'}='signal_cleanup';\n $SIG{'SIGUSR\
+2'}='signal_cleanup';\n\n $SIG{'SIGSYS'}='sig\
+nal_cleanup';\n $SIG{'SIGURG'}='signal_cleanu\
+p';\n $SIG{'SIGCHLD'}='signal_cleanup';\n \
+ $SIG{'SIGXCPU'}='signal_cleanup';\n $SIG{'S\
+IGWINCH'}='signal_cleanup';\n \n $SIG{'I\
+NT'}='signal_cleanup';\n $SIG{'TERM'}='signal\
+_cleanup';\n $SIG{'KILL'}='signal_cleanup';\n\
+ $SIG{'QUIT'}='signal_cleanup';\n \n \
+ our $debug_lock=$ENV{\"DEBUG_LOCK\"};\n \n \
+ \n \n \n foreach my $a (@ARGV)\
+{$CL.=\" $a\";}\n if ( $debug_lock ){print ST\
+DERR \"\\n\\n\\n********** START PG: $PROGRAM ****\
+*********\\n\";}\n if ( $debug_lock ){print S\
+TDERR \"\\n\\n\\n**********(tcg) LOCKDIR: $LOCKDIR\
+ $$ *************\\n\";}\n if ( $debug_lock )\
+{print STDERR \"\\n --- $$ -- $CL\\n\";}\n \n\
+ \n \n \n }\nsub flush_error\n \
+{\n my $msg=shift;\n return add_error ($EXIT\
+_FAILURE,$$, $$,getppid(), $msg, $CL);\n }\nsub a\
+dd_error \n {\n my $code=shift;\n my $rpid=\
+shift;\n my $pid=shift;\n my $ppid=shift;\n \
+ my $type=shift;\n my $com=shift;\n \n \
+$ERROR_DONE=1;\n lock4tc ($rpid, \"LERROR\",\"L\
+SET\",\"$pid -- ERROR: $type\\n\");\n lock4tc (\
+$$, \"LERROR\",\"LSET\", \"$pid -- COM: $com\\n\")\
+;\n lock4tc ($$, \"LERROR\",\"LSET\", \"$pid --\
+ STACK: $ppid -> $pid\\n\");\n \n return $cod\
+e;\n }\nsub add_warning \n {\n my $rpid=shift\
+;\n my $pid =shift;\n my $command=shift;\n \
+ my $msg=\"$$ -- WARNING: $command\\n\";\n pri\
+nt STDERR \"$msg\";\n lock4tc ($$, \"LWARNING\"\
+, \"LSET\", $msg);\n }\n\nsub signal_cleanup\n {\
+\n print dtderr \"\\n**** $$ (tcg) was killed\\\
+n\";\n &cleanup;\n exit ($EXIT_FAILURE);\n \
+}\nsub clean_dir\n {\n my $dir=@_[0];\n if \
+( !-d $dir){return ;}\n elsif (!($dir=~/tmp/)){\
+return ;}#safety check 1\n elsif (($dir=~/\\*/)\
+){return ;}#safety check 2\n else\n {\n `r\
+m -rf $dir`;\n }\n return;\n }\nsub clean\
+up\n {\n #print stderr \"\\n----tc: $$ Kills $\
+PIDCHILD\\n\";\n #kill (SIGTERM,$PIDCHILD);\n \
+ my $p=getppid();\n $CLEAN_EXIT_STARTED=1;\n \
+ \n \n \n if (&lock4tc($$,\"LERROR\", \"\
+LCHECK\", \"\"))\n {\n my $ppid=getppid();\n \
+if (!$ERROR_DONE) \n {\n &lock4tc($$,\"LERRO\
+R\", \"LSET\", \"$$ -- STACK: $p -> $$\\n\");\n \
+ &lock4tc($$,\"LERROR\", \"LSET\", \"$$ -- COM: $\
+CL\\n\");\n }\n }\n my $warning=&lock4tc\
+($$, \"LWARNING\", \"LREAD\", \"\");\n my $erro\
+r=&lock4tc($$, \"LERROR\", \"LREAD\", \"\");\n \
+ #release error and warning lock if root\n \n \
+ if (isrootpid() && ($warning || $error) )\n \
+ {\n \n print STDERR \"**************** Summary **\
+***********\\n$error\\n$warning\\n\";\n\n &lock4tc\
+($$,\"LERROR\",\"RELEASE\",\"\");\n &lock4tc($$,\"\
+LWARNING\",\"RELEASE\",\"\");\n } \n \n \
+ \n foreach my $f (@TMPFILE_LIST)\n {\n if\
+ (-e $f){unlink ($f);} \n }\n foreach my $\
+d (@TMPDIR_LIST)\n {\n clean_dir ($d);\n \
+ }\n #No More Lock Release\n #&lock4tc($$,\"\
+LLOCK\",\"LRELEASE\",\"\"); #release lock \n\n \
+if ( $debug_lock ){print STDERR \"\\n\\n\\n*******\
+*** END PG: $PROGRAM ($$) *************\\n\";}\n \
+ if ( $debug_lock ){print STDERR \"\\n\\n\\n*****\
+*****(tcg) LOCKDIR: $LOCKDIR $$ *************\\n\"\
+;}\n }\nEND \n {\n \n &cleanup();\n }\n \
+ \nsub blast_com2new_blast_com\n {\n my $c\
+om=shift;\n if ($ENV{\"NCBI_BLAST_4_TCOFFEE\"\
+} eq \"OLD\"){return $com;}\n elsif (!&pg_is_\
+installed(\"legacy_blast.pl\")){return $com;}\n \
+ else \n {\n if ($com=~/formatdb/)\n {\n \
+ $com=~s/formatdb/makeblastdb/;\n $com=~\
+s/\\-i/\\-in/;\n if ($com =~/pF/){$com=~s/\\\
+-pF/\\-dbtype nucl/;}\n if ($com =~/p F/){$c\
+om=~s/\\-p F/\\-dbtype nucl/;}\n $com=\"$com\
+ -logfile /dev/null\";\n return $com;\n \
+}\n elsif (&is_blast_package($com))\n {\n \
+ my $path;\n \n if ( $ENV{\"NCBI_BI\
+N_4_TCOFFEE\"}){$path=$ENV{\"NCBI_BLAST_4_TCOFFEE\\
+"};}\n else\n {\n $path=`which legacy_bl\
+ast.pl`;\n $path=~s/\\/legacy_blast\\.pl//;\n \
+ chomp ($path);\n }\n $path=\"--path $path\
+\";\n if ( $com=~/\\>\\>/){$com=~s/\\>\\>/ $\
+path \\>\\>/;}\n elsif ( $com=~/\\>/){$com=~\
+s/\\>/ $path \\>/;}\n else {$com.=\" $path\"\
+;}\n $com=\"legacy_blast.pl $com\";\n \
+\n return $com;\n }\n }\n }\nsub safe\
+_system \n{\n my $com=shift;\n my $ntry=shift;\n\
+ my $ctry=shift;\n my $pid;\n my $status;\n my\
+ $ppid=getppid();\n if ($com eq \"\"){return 1;}\\
+n \n if ( ($com=~/^blast/) ||($com=~/^formatdb/)\
+){$com=&blast_com2new_blast_com($com);} \n\n if (\
+($pid = fork ()) < 0){return (-1);}\n if ($pid ==\
+ 0)\n {\n set_lock($$, \" -SHELL- $com (tc\
+g)\");\n if( $debug_cmd_exec ) { printf \"exe\
+c: %s\\n\", $com; } \n exec ($com);\n }\n \
+ else\n {\n lock4tc ($$, \"LLOCK\", \"LSET\
+\", \"$pid\\n\");#update parent\n $PIDCHILD=$\
+pid;\n }\n if ($debug_lock){printf STDERR \"\\\
+n\\t .... safe_system (fasta_seq2hmm) p: $$ c: $p\
+id COM: $com\\n\";}\n\n waitpid ($pid,WTERMSIG);\\
+n\n shift_lock ($pid,$$, \"LWARNING\",\"LWARNING\\
+", \"LSET\");\n\n if ($? == $EXIT_FAILURE || lock\
+4tc($pid, \"LERROR\", \"LCHECK\", \"\"))\n {\n \
+ if ($ntry && $ctry <$ntry)\n {\n\n add_warn\
+ing ($$,$$,\"$com failed [retry: $ctry out of $ntr\
+y]\");\n lock4tc ($pid, \"LRELEASE\", \"LERROR\"\
+, \"\");\n #if ($com=~/EBI/){$com=~s/EBI/NCBI/;}\
+\n #elsif ($com=~/NCBI/){$com=~s/NCBI/EBI/;}\n \
+ \n return safe_system ($com, $ntry, ++$ctry);\n\
+ }\n elsif ($ntry == -1)\n {\n if (!shift_l\
+ock ($pid, $$, \"LERROR\", \"LWARNING\", \"LSET\")\
+)\n {\n add_warning ($$,$$,\"$com failed\
+\");\n }\n else\n {\n lock4tc ($pi\
+d, \"LRELEASE\", \"LERROR\", \"\");\n }\n re\
+turn $?;}\n else\n {\n if (!shift_lock ($pi\
+d,$$, \"LERROR\",\"LERROR\", \"LSET\"))\n {\n \
+ myexit(add_error ($EXIT_FAILURE,$$,$pid,getp\
+pid(), \"UNSPECIFIED system\", $com));\n }\n }\
+\n }\n return $?;\n}\n\nsub check_configuratio\
+n \n {\n my @l=@_;\n my $v;\n fo\
+reach my $p (@l)\n {\n \n if ( $p eq \"EMAIL\
+\")\n { \n if ( !($EMAIL=~/@/))\n {\n \
+add_warning($$,$$,\"Could Not Use EMAIL\");\n mye\
+xit(add_error ($EXIT_FAILURE,$$,$$,getppid(),\"EMA\
+IL\",\"$CL\"));\n }\n }\n elsif( $p eq\
+ \"INTERNET\")\n {\n if ( !&check_intern\
+et_connection())\n {\n myexit(add_error ($EXIT\
+_FAILURE,$$,$$,getppid(),\"INTERNET\",\"$CL\"));\n\
+ }\n }\n elsif( $p eq \"wget\")\n {\n \
+ if (!&pg_is_installed (\"wget\") && !&pg_is_i\
+nstalled (\"curl\"))\n {\n myexit(add_error ($\
+EXIT_FAILURE,$$,$$,getppid(),\"PG_NOT_INSTALLED:wg\
+et\",\"$CL\"));\n }\n }\n elsif( !(&pg_is_i\
+nstalled ($p)))\n {\n myexit(add_error (\
+$EXIT_FAILURE,$$,$$,getppid(),\"PG_NOT_INSTALLED:$\
+p\",\"$CL\"));\n }\n }\n return 1;\n }\
+\n\n$program=\"T-COFFEE (r550)\";\n\n","*TC_METHOD\
+_FORMAT_01\n******************generic_method.tc_me\
+thod*************\n*\n* Incorporating new me\
+thods in T-Coffee\n* Cedric Notredame 26/08/\
+08\n*\n*******************************************\
+************\n*This file is a method file\n*Copy i\
+t and adapt it to your need so that the method \n*\
+you want to use can be incorporated within T-Coffe\
+e\n***********************************************\
+********\n* USAGE \
+ *\n*********************************\
+**********************\n*This file is passed to t_\
+coffee via -in:\n*\n* t_coffee -in Mgeneric_method\
+.method\n*\n* The method is passed to the shell us\
+ing the following\n*call:\n*<EXECUTABLE><PARAM1><I\
+N_FLAG><seq_file><PARAM2><OUT_FLAG><outname><PARAM\
+>\n*\n*Conventions:\n*<FLAG_NAME> <TYPE> <VALUE>\
+\n*<VALUE>: no_name <=> Replaced with a space\n*<\
+VALUE>:   <=> Replaced with a space\n*\n******\
+*************************************************\\
+n* ALN_MODE \
+ *\n******************************************\
+*************\n*pairwise ->all Vs all (no self )\
+[(n2-n)/2aln]\n*m_pairwise ->all Vs all (no self)[\
+n^2-n]^2\n*s_pairwise ->all Vs all (self): [n^2-n]\
+/2 + n\n*multiple ->All the sequences in one go\\
+n*\nALN_MODE pairwise\n*\n***********************\
+********************************\n* \
+ OUT_MODE *\n*********\
+**********************************************\n* \
+mode for the output:\n*External methods: \n* aln -\
+> alignmnent File (Fasta or ClustalW Format)\n* li\
+b-> Lib file (TC_LIB_FORMAT_01)\n*Internal Methods\
+:\n* fL -> Internal Function returning a List (Lib\
+rairie)\n* fA -> Internal Function returning an Al\
+ignmnent\n*\nOUT_MODE aln\n**********************\
+*********************************\n* \
+ SEQ_TYPE *\n********\
+***********************************************\n*\
+G: Genomic, S: Sequence, P: PDB, R: Profile\n*Exam\
+ples:\n*SEQTYPE S sequences against sequences (def\
+ault)\n*SEQTYPE S_P sequence against structure\n*S\
+EQTYPE P_P structure against structure\n*SEQTYPE P\
+S mix of sequences and structure \n*\nSEQ_TYPE S\n\
+*\n\n*********************************************\
+**********\n* COMMAND LINE \
+ *\n*EXECUTABLE PARAM1 IN_FLAG OUT_\
+FLAG PARAM *\n************************\
+*******************************\n*****************\
+**************************************\n* \
+ EXECUTABLE *\n***\
+**************************************************\
+**\n*name of the executable\n*passed to the shell:\
+ executable\n* \nEXECUTABLE tc_generic_method.pl\n\
+*\n***********************************************\
+********\n* IN_FLAG \
+ *\n********************************\
+***********************\n*IN_FLAG\n*flag indicatin\
+g the name of the in coming sequences\n*IN_FLAG S \
+no_name ->no flag\n*IN_FLAG S &bnsp-in&bnsp -> \" \
+-in \"\n*\nIN_FLAG -infile=\n*\n*****************\
+**************************************\n* \
+ OUT_FLAG *\n***\
+**************************************************\
+**\n*OUT_FLAG\n*flag indicating the name of the ou\
+t-coming data\n*same conventions as IN_FLAG\n*OUT_\
+FLAG S no_name ->no flag\n*if you want to redirect\
+, pass the parameters via PARAM1\n*set OUT_FLAG to\
+ >\n*\nOUT_FLAG -outfile=\n*\n*******************\
+************************************\n* \
+ PARAM_1 *\n***\
+**************************************************\
+**\n*<EXECUTABLE><PARAM1><IN_FLAG><seq_file><PARAM\
+2><OUT_FLAG><outname><PARAM>\n*Parameters sent to \
+the EXECUTABLE and specified *before* IN_FLAG \n*I\
+f there is more than 1 PARAM line, the lines are\n\
+*concatenated\n*Command_line: @EP@PARAM@-gapopen%e\
+10%s-gapext%e20\n* %s white space\n* %e equal sign\
+\n*\n*PARAM1 \n*\n*\n*\n**************************\
+*****************************\n* \
+PARAM_2 *\n**********\
+*********************************************\n*<E\
+XECUTABLE><PARAM1><IN_FLAG><seq_file><PARAM2><OUT_\
+FLAG><outname><PARAM>\n*Parameters sent to the EXE\
+CUTABLE and specified \n*after* IN_FLAG and *befor\
+e* OUT_FLAG\n*If there is more than 1 PARAM line, \
+the lines are\n*concatenated\n*\n*PARAM1 \n*\n*\n*\
+**************************************************\
+****\n* PARAM \
+ *\n*************************************\
+******************\n*<EXECUTABLE><PARAM1><IN_FLAG>\
+<seq_file><PARAM2><OUT_FLAG><outname><PARAM>\n*Par\
+ameters sent to the EXECUTABLE and specified *afte\
+r* OUT_FLAG\n*If there is more than 1 PARAM line, \
+the lines are\n*concatenated\n*\nPARAM -mode=seq_m\
+sa -method=clustalw\nPARAM -OUTORDER=INPUT -NEWT\
+REE=core -align -gapopen=-15\n*\n*****************\
+**************************************\n* \
+ END *\n***\
+**************************************************\
+**\n","*TC_METHOD_FORMAT_01\n***************clusta\
+lw_method.tc_method*********\nEXECUTABLE clustalw\\
+nALN_MODE pairwise\nIN_FLAG -INFILE=\nOUT_FLAG \
+-OUTFILE=\nOUT_MODE aln\nPARAM -gapopen=-10\nSEQ\
+_TYPE S\n****************************************\
+*********\n","$VersionTag = \
+ \
+ \
+ 2.43;\nuse Env;\nuse FileHandle;\nuse Cwd;\
+\nuse File::Path;\nuse Sys::Hostname;\nour $PIDCHI\
+LD;\nour $ERROR_DONE;\nour @TMPFILE_LIST;\nour $EX\
+IT_FAILURE=1;\nour $EXIT_SUCCESS=0;\n\nour $REFDIR\
+=getcwd;\nour $EXIT_SUCCESS=0;\nour $EXIT_FAILURE=\
+1;\n\nour $PROGRAM=\"extract_from_pdb\";\nour $CL=\
+$PROGRAM;\n\nour $CLEAN_EXIT_STARTED;\nour $debug_\
+lock=$ENV{\"DEBUG_LOCK\"};\nour $LOCKDIR=$ENV{\"LO\
+CKDIR_4_TCOFFEE\"};\nif (!$LOCKDIR){$LOCKDIR=getcw\
+d();}\nour $ERRORDIR=$ENV{\"ERRORDIR_4_TCOFFEE\"};\
+\nour $ERRORFILE=$ENV{\"ERRORFILE_4_TCOFFEE\"};\n&\
+set_lock ($$);\nif (isshellpid(getppid())){lock4tc\
+(getppid(), \"LLOCK\", \"LSET\", \"$$\\n\");}\n \
+ \nour $SILENT=\" >/dev/null 2>/dev/null\";\nour\
+ $INTERNET=-1;\n\n\n\n\n\n\n\nour $BLAST_MAX_NRUNS\
+=2;\nour $EXIT_SUCCESS=0;\nour $EXIT_FAILURE=1;\no\
+ur $CONFIGURATION=-1;\nour $REF_EMAIL=\"\";\nour $\
+PROGRAM=\"extract_from_pdb\";\n\n\nmy %onelett_pro\
+t=&fill_onelett_prot();\nmy %threelett_prot=&fill_\
+threelett_prot();\nmy %onelett_RNA=&fill_onelett_R\
+NA();\nmy %threelett_RNA=&fill_threelett_RNA();\nm\
+y %onelett_DNA=&fill_onelett_DNA();\nmy %threelett\
+_DNA=&fill_threelett_DNA();\n\n\n\n\n\nmy %onelett\
+ = (\n'P' => \\%onelett_prot,\n'D' => \\%onelett_D\
+NA,\n'R' => \\%onelett_RNA\n);\n\n\nmy %threelett \
+= (\n'P' => \\%threelett_prot,\n'D' => \\%threelet\
+t_DNA,\n'R' => \\%threelett_RNA\n);\n\n\n\n\n\n\n\\
+nif($ARGV[0]=~/help/ ||$ARGV[0]=~/man/ || $ARGV[0]\
+=~/HELP/ || $ARGV[0]=~/Man/ || $ARGV[0] eq \"-h\" \
+ || $ARGV[0] eq \"-H\" )\n{die \"SYNTAX: extract_\
+from_pdb Version $VersionTag \n Minimum: \
+ [extract_from_pdb file] \n OR \n [.\
+.. | extract_from_pdb]\n Flags (Default setting o\
+n the first line)\n -version...................\
+[Returns the Version Number]\n -force...\
+..................[Forces the file to be treated l\
+ike a PDB file]\n \
+ [Regenerates the header and SEQRES fields]\n \
+ -force_name................[Forces the f\
+ile to be named after name]]\n -infile..\
+...file...........[Flag can be omited]\n \
+ [File must be pdb or fro pgm]\n \
+ [File can also be compre\
+ssed Z or gz]\n \
+ [In the case of a compressed file, you can omit\
+ the gz|Z extension]\n -netfile.........\
+..........[File will be fetch from the net using w\
+get]\n [wget \
+or curl must be installed]\n \
+ [ftp://ftp.gnu.org/pub/gnu/wget/]\\
+n [http://cur\
+l.haxx.se/]\n \
+ [Must also be used to retrieve the file from a lo\
+cal pdb copy (cf netaddress)]\n -netaddr\
+ess................[Address used for the retrievin\
+g the netfile]\n \
+ [http://www.rcsb.org/pdb/cgi/export.cgi/%%.pdb\
+.gz?format=PDB&pdbId=%%&compression=gz]\n \
+ [http://www.expasy.ch\
+/cgi-bin/get-pdb-entry.pl?%%]\n \
+ [local -> will get the file fro\
+m pdb_dir (see pdb_dir)]\n -netcompressi\
+on............[Extension if the netfile comes comp\
+ressed]\n [gz\
+]\n -pdb_dir...................[address \
+of the repertory where the pdb is installed]\n \
+ [Supports standa\
+rd ftp style installation OR every stru in DIR]\n \
+ [Give the ...\
+./pdb/structure/ dir]\n \
+ [If value omitted, the pg gets it from \
+the env variable PDB_DIR]\n -netcompress\
+ion_pg.........[gunzip]\n -is_pdb_name..\
+........name.[Returns 1 if the name is a PDB ID, 0\
+ otherwise]\n -model_type...........name\
+.[Returns the model type if valid PDB name]\n \
+ -is_released_pdb_name name.[Returns 1 if the\
+ name corresponds to a released PDB file]\n \
+ -get_pdb_chains.....name...[Returns the list o\
+f chains corresponding to the entry]\n -\
+get_pdb_id.........name...[Returns the PDB id with\
+in the provided pdb file]\n -get_fugue_n\
+ame.....name...[Turns a name into a name valid for\
+ fugue]\n [Us\
+es the netaddress to do so]\n -chain......FIRST\
+..........[Extract the first chain only]\n \
+ A B C..........[Extract Several chains if needed]\
+\n ALL............[Extract all the chains]\
+ \n -ligand.....ALL............[Extract \
+the ligands in the chain (HETATM)]\n \
+ <name1>,<name2>[Extract All the named lig\
+nds]\n -ligand_only...............[Extract only\
+ the ligands]\n -ligand_list............\
+...[Extract the list of ligands]\n -coor.......\
+<start>..<end>.[Coordinates of the fragment to ext\
+ract]\n [Omit end to include the C\
+ter]\n -num........absolute.......[absol\
+ute: relative to the seq] \n \
+ file...........[file: relative to file]\n \
+ -num_out....new............[new: start 1->L]\n \
+ old............[old: keep th\
+e file coordinates]\n -delete.....<start\
+>..<end>.[Delete from residue start to residue end\
+]\n -atom.......CA.............[Atoms to includ\
+e, ALL for all of them]\n CA O N.........[\
+Indicate several atoms if needed]\n -code......\
+.3..............[Use the 1 letter code or the 3 le\
+tters code]\n -mode.......raw............[Outpu\
+t original pdb file]\n pdb..\
+..........[Output something that looks like pdb]\n\
+ fasta..........[Output the sequences in f\
+asta format]\n simple.........[Output a fo\
+rmat easy to parse in C ]\n -seq_field.\
+.ATOM...........[Field used to extract the sequenc\
+e]\n SEQRES.........[Use the complete sequ\
+ence]\n -seq.......................[Equivalent \
+to -mode fasta]\n -model......1..............[\
+Chosen Model in an NMR file]\n -nodiagno\
+stic..............[Switches Error Messages off]\n \
+ -debug.....................[Sets the DEB\
+UG ON]\n -no_remote_pdb_dir.........[Do \
+not look for a remote file]\n -cache_pdb\
+.................[Cache Value, default is $HOME/.t\
+_coffee/cache, other values: NO<=> No cache]\n\n \
+ Environement Variables\n These varia\
+bles can be set from the environement\n \
+Command line values with the corresponding flag su\
+perseed evironement value\n NO_REMOTE_PD\
+B_DIR..........[Prevents the program from searchin\
+g remote file: faster]\n PDB_DIR........\
+............[Indicates where PDB file must be fetc\
+hed (localy)]\n\n PROBLEMS: please contact cedric\
+.notredame\\@europe.com\\n\";\n exit ($EXIT_SUCCE\
+SS);\n}\n\n$np=0;\n$n_para=$#ARGV;\n$model=1;\n$pd\
+b_dir=$ENV{'PDB_DIR'};if ($pdb_dir){$pdb_dir.=\"/\\
+";}\n$debug=$ENV{'DEBUG_EXTRACT_FROM_PDB'};\n\n$no\
+_remote_pdb_dir=$ENV{NO_REMOTE_PDB_DIR};\n$HOME=$E\
+NV{'HOME'};\nif ( $ENV{CACHE_4_TCOFFEE})\n{$cache=\
+$ENV{CACHE_4_TCOFFEE};}\nelse\n{\n $cache=\"$HO\
+ME/.t_coffee/cache/\";\n}\n\n \n$netaddress=\"ht\
+tp://www.rcsb.org/pdb/files/%%.pdb.gz\";\n$netcomp\
+ression_pg=\"gunzip\";\n$netcompression=\"gz\";\n\\
+nforeach ($np=0; $np<=$n_para; $np++)\n { \
+\n $value=$ARGV[$np];\n \n if ($np==0 && \
+!($value=~/^-.*/))\n { \n $pdb_file= $ARGV[$n\
+p];\n }\n elsif ( !($value=~/^-.*/))\n \
+ {\n print \"@ARGV\";\n die;\n } \n \n \
+ elsif ($value eq \"-nodiagnostic\"){$nodiagnostic\
+=1;}\n elsif ($value eq \"-force\")\n {\n \
+$force_pdb=1;\n }\n elsif ($value eq \"-fo\
+rce_name\")\n {\n $force_name=$ARGV[++$np];\n\
+ $force_pdb=1;\n }\n \n elsif ($value e\
+q \"-is_pdb_name\")\n {\n $pdb_file= $ARGV[++\
+$np]; \n $is_pdb_name=1; \n } \n elsif ($v\
+alue eq \"-is_released_pdb_name\")\n {\n $pdb\
+_file= $ARGV[++$np]; \n $is_released_pdb_name=1;\n\
+ }\n elsif ($value eq \"-model_type\")\n \
+ {\n $pdb_file= $ARGV[++$np]; \n $model_type=1;\
+\n }\n elsif ($value eq \"-debug\")\n{\n $\
+debug=1;\n}\n elsif ($value eq \"-get_pdb_chain\
+s\")\n{\n $pdb_file= $ARGV[++$np];\n $get_pdb_chai\
+ns=1;\n}\n elsif ($value eq \"-get_pdb_ligands\\
+")\n{\n $get_pdb_ligands=1;\n}\n \n elsif ($\
+value eq \"-get_pdb_id\")\n{\n $pdb_file= $ARGV[++\
+$np];\n $get_pdb_id=1;\n \n}\n \n elsif ( $v\
+alue eq \"-get_fugue_name\")\n{\n $pdb_file= $ARGV\
+[++$np];\n $get_fugue_name=1;\n}\n elsif ( $val\
+ue eq \"-infile\")\n{\n $pdb_file= $ARGV[++$\
+np];\n} \n elsif ($value eq \"-netfile\")\n{\n \
+$netfile=1;\n if ( !($ARGV[$np+1]=~/^-.*/)){$pdb_f\
+ile= $ARGV[++$np];}\n}\n elsif ( $value eq \"-\
+num\")\n{\n $numbering= $ARGV[++$np];\n}\n \
+ elsif ( $value eq \"-num_out\")\n{\n $num\
+bering_out= $ARGV[++$np];\n}\n elsif ( $value e\
+q \"-netaddress\")\n{\n $netadress=$ARGV[++$np];\n\
+}\n \n elsif ( $value eq \"-netcompression\\
+")\n{\n $netcompression=$ARGV[++$np];\n}\n els\
+if ( $value eq \"-pdb_dir\")\n{\n if ( !($ARGV[$n\
+p+1]=~/^-.*/)){$pdb_dir= \"$ARGV[++$np]/\";}\n}\n \
+ elsif ( $value eq \"-no_remote_pdb_dir\")\n{\n\
+ $no_remote_pdb_dir=1;\n if ( !($ARGV[$np+1]=~/^-.\
+*/)){$pdb_dir= \"$ARGV[++$np]/\";}\n}\n elsif (\
+ $value eq \"-cache\")\n{\n $cache=$ARGV[++$np];\n\
+}\n \n elsif ($value eq \"-netcompression_pg\
+\")\n{\n $netcompression_pg=$ARGV[++$np];\n}\n \
+ elsif ($value eq \"-mode\")\n{\n $MODE=$A\
+RGV[++$np];\n}\n\n elsif ( $value eq \"-model\"\
+)\n{\n $model= $ARGV[++$np];\n}\n elsif (\
+$value eq \"-seq_field\" )\n{\n $seq_field= \
+$ARGV[++$np];\n} \n elsif ($value eq \"-coor\\
+" )\n{\n $start= $ARGV[++$np];\n \n i\
+f (($ARGV[$np+1] eq \"\") ||($ARGV[$np+1]=~/^-.*/)\
+){$end=\"*\";} \n else {$end= $ARGV[++$np]\
+;} \n $coor_set=1;\n}\n elsif ($value\
+ eq \"-delete\" )\n{\n $delete_start= $ARGV[\
+++$np];\n $delete_end= $ARGV[++$np];\n \
+ $delete_set=1;\n}\n elsif ($value eq \"-code\\
+")\n{\n $code= $ARGV[++$np];\n}\n elsif \
+($value eq \"-no_hetatm\")\n{\n $no_hetatm=1\
+;\n}\n elsif ($value eq \"-chain\")\n{\n \
+while (!($ARGV[$np+1] eq \"\") &&!($ARGV[$np+1]=~/\
+^-.*/))\n{\n ++$np;\n @c_chain=(@chain\
+, $ARGV[$np]);\n $hc_chain{$ARGV[$np]}=$#c_\
+chain+1;\n} \n}\n elsif ($value eq \"\
+-atom\")\n{\n\n while (!($ARGV[$np+1] eq \"\\
+") && !($ARGV[$np+1]=~/^-.*/))\n{\n ++$np;\n\
+ $atom[$n_atom++]= $ARGV[$np];\n $ato\
+m_list{$ARGV[$np]}=1; \n} \n \n}\n \
+elsif ( $value eq \"-unfold\")\n{\n $unfold=1;\n}\\
+n elsif ($value eq \"-seq\" ||$value eq \"-fast\
+a\" )\n{\n $MODE=\"fasta\";\n}\n elsif ( \
+$value eq \"-version\")\n{\n print STDERR \"\\nex\
+tract_from_pdb: Version $VersionTag\\n\";\n &myexi\
+t ($EXIT_SUCCESS);\n}\n elsif ( $value eq \"-li\
+gand\")\n{\n while (!($ARGV[$np+1] eq \"\") && !($\
+ARGV[$np+1]=~/^-.*/))\n{\n ++$np;\n $ligan\
+d=1;\n $ligand_list{$ARGV[$np]}=1; \n} \\
+n $hc_chain{'LIGAND'}=1;\n}\n elsif ( $value eq\
+ \"-ligand_only\")\n{\n $ligand_only=1;\n}\n}\nif \
+( $debug)\n{\n print STDERR \"\\n[DEBUG:extract\
+_from_pdb] NO_REMOTE_PDB_DIR: $no_remote_pdb_dir\\\
+n\";\n print STDERR \"\\n[DEBUG:extract_from_pd\
+b] PDB_DIR: $pdb_dir\\n\";\n}\n\n\nif ( $is_pdb_na\
+me)\n {\n if (&remote_is_pdb_name($pdb_file))\\
+n {\n print \"1\";\n }\n else\n \
+{\n print \"0\";\n }\n exit ($EXIT_SUCCESS\
+);\n }\n\nif ( $is_released_pdb_name)\n {\n \\
+n if (&is_released($pdb_file))\n {\n print\
+ \"1\";\n }\n else\n {\n print \"0\";\
+\n }\n exit ($EXIT_SUCCESS);\n }\nif ($mo\
+del_type)\n {\n \n printf \"%s\", &pdb2model\
+_type($pdb_file);\n exit ($EXIT_SUCCESS);\n \
+\n }\n \n\nif (!$force_name)\n{\n $pdb_file\
+=~/([^\\/]*)$/;\n $force_name=$1;\n}\n\n$local_\
+pdb_file=$pdb_file;\n\nif ( $debug){print STDERR \\
+"\\n[DEBUG: extract_from_pdb] Scan For $local_pdb_\
+file\\n\";}\n\n$mem=$no_remote_pdb_dir;\n$no_remot\
+e_pdb_dir=1;\n$tmp_pdb_file=get_pdb_file ($local_p\
+db_file);\n\nif ( !-e $tmp_pdb_file || $tmp_pdb_fi\
+le eq \"\")\n {\n $local_pdb_file=$pdb_file;\n\
+ ($local_pdb_file, $suffix_chain)=&pdb_name2nam\
+e_and_chain($local_pdb_file);\n\n if ($local_pd\
+b_file)\n {\n if ( $debug){print STDERR \"\\n\
+Split $pdb_file into $local_pdb_file and $suffix_c\
+hain \\n\";}\n $tmp_pdb_file=get_pdb_file ($local_\
+pdb_file);\n if ( $tmp_pdb_file ne \"\")\n {\n \
+ @c_chain=();\n @c_chain=($suffix_chain);\n \
+ %hc_chain=();\n $hc_chain{$suffix_chain}=1\
+;\n }\n }\n }\n\n$no_remote_pdb_dir=$mem;\\
+nif ($no_remote_pdb_dir==0)\n {\n \n if ( !\
+-e $tmp_pdb_file || $tmp_pdb_file eq \"\")\n \
+{\n \n $local_pdb_file=$pdb_file;\n ($local_pdb_fi\
+le, $suffix_chain)=&pdb_name2name_and_chain($local\
+_pdb_file);\n if ($local_pdb_file)\n {\n \n \
+ if ( $debug){print STDERR \"\\nSplit $pdb_file\
+ into $local_pdb_file and $suffix_chain \\n\";}\n \
+ \n $tmp_pdb_file=get_pdb_file ($local_pdb_\
+file); \n \n if ( $tmp_pdb_file ne \"\"\
+)\n {\n @c_chain=();\n @c_chain=($suffix_c\
+hain);\n %hc_chain=();\n $hc_chain{$suffix_chain\
+}=1;\n }\n }\n }\n }\n\nif ( $debug)\
+{print STDERR \"\\n$pdb_file copied into ##$tmp_pd\
+b_file##\\n\";}\n\nif ( !-e $tmp_pdb_file || $tmp_\
+pdb_file eq \"\")\n{\n if ($is_pdb_name)\n{\n \
+print \"0\\n\"; exit ($EXIT_SUCCESS);\n}\n else\n{\
+\n \n print \"\\nEXTRACT_FROM_PDB: NO RESULT \
+for $pdb_file\\n\";\n &myexit ($EXIT_SUCCESS);\
+ \n}\n}\n\n\n\n\n%molecule_type=&pdbfile2chaintype\
+($tmp_pdb_file);\nif ( $debug){print STDERR \"\\n\\
+\tSequence Type determined\\n\";}\n\n$pdb_id=&get_\
+pdb_id ($tmp_pdb_file);\nif ( $debug){print STDERR\
+ \"\\n\\tID: $pdb_id (for $tmp_pdb_file)\\n\";}\n\\
+nif ( $pdb_id eq \"\"){$pdb_id=$force_name;}\n\n@f\
+_chain=&get_chain_list ($tmp_pdb_file);\nif ( $deb\
+ug){print STDERR \"\\n\\tChain_list:@f_chain\\n\";\
+}\n\nif ( $get_pdb_chains)\n{\n print \"@f_chai\
+n\\n\";\n &myexit ($EXIT_SUCCESS);\n}\nif ( $ge\
+t_pdb_ligands)\n{\n %complete_ligand_list=&get_\
+ligand_list ($tmp_pdb_file);\n print $complete_\
+ligand_list{\"result\"};\n &myexit ($EXIT_SUCCE\
+SS);\n}\n\nelsif ( $get_pdb_id ||$get_fugue_name )\
+\n{\n if (@c_chain && $c_chain[0] eq \"FIRST\
+\"){$pdb_id=$pdb_id.$f_chain[0];}\n elsif (@c_c\
+hain && $c_chain[0] ne \" \"){$pdb_id=$pdb_id.$c_c\
+hain[0];}\n \n print \"$pdb_id\\n\";\n &m\
+yexit ($EXIT_SUCCESS);\n \n}\nelsif ( $is_pdb_n\
+ame)\n{\n printf \"1\\n\";\n &myexit ($EXIT_\
+SUCCESS);\n}\n\n\n\n$structure_file=vtmpnam();\n\n\
+if ( $debug){print STDERR \"\\n\\tCheck_point #1: \
+$tmp_pdb_file $structure_file\\n\";}\n\n$INFILE=v\
+fopen (\"$tmp_pdb_file\", \"r\"); \n$TMP=vfopen (\\
+"$structure_file\", \"w\");\n\n$print_model=1;\n$i\
+n_model=0;\n\nif ( $debug){print STDERR \"\\n\\tCh\
+eck_point #2\\n\";}\nwhile ( <$INFILE>)\n{\n my $\
+first_model=0;\n $line=$_;\n\n if ( !$first_mode\
+l && ($line =~/^MODEL\\s*(\\d*)/))\n {\n $\
+first_model=$1;\n if ($model==1){$model=$firs\
+t_model;}\n }\n \n if (($line =~/^MODEL\\s*(\\
+\d*)/))\n {\n if ($1==$model)\n {\n $in_\
+model=1;\n $print_model=1;\n $is_nmr=1;\n }\n \
+ elsif ( $in_model==0)\n {\n $print_model=0;\
+\n }\n elsif ( $in_model==1)\n {\n last;\n \
+}\n }\n if ($print_model){print $TMP $line;} \
+\n}\nclose ($TMP);\nclose ($INFILE);\n\nif ( $debu\
+g){print STDERR \"\\n\\tCheck_point #3\\n\";} \n\n\
+ if ($numbering eq \"\"){$numbering=\"absolute\";\
+}\n if ($numbering_out eq \"\"){$numbering_out=\"\
+new\";}\n\n if ( $delete_set && $coor_set) {die \\
+"-delete and -coor are mutually exclusive, sorry\\\
+n\";}\n if ( $n_atom==0){$atom_list[$n_atom++]=\"\
+ALL\";$atom_list{$atom_list[0]}=1;}\n if ( $seq_f\
+ield eq \"\"){$seq_field=\"ATOM\";}\n \n if ( $M\
+ODE eq \"\"){$MODE=\"pdb\";}\n elsif ( $MODE eq \\
+"simple\" && $code==0){$code=1;}\n\n if ( $code==\
+0){$code=3;}\n\n\nif ($f_chain[0] eq \" \"){$hc_ch\
+ain{' '}=1;$c_chain[0]=\" \";}\nelsif (!@c_chain){\
+$hc_chain{FIRST}=1;$c_chain[0]=\"FIRST\";}#make su\
+re the first chain is taken by default\n\nif ($\
+hc_chain{ALL}) \n{\n @c_chain=@f_chain;\n \
+ foreach $e (@c_chain){$hc_chain{$e}=1;}\n}\nelsi\
+f($hc_chain{FIRST})\n{\n @c_chain=($f_chain[0]);\n\
+ $hc_chain{$f_chain[0]}=1;\n}\n\n\n$MAIN_HOM_CODE=\
+&get_main_hom_code ($structure_file);\n$INFILE=vfo\
+pen ($structure_file, \"r\");\n\n\nif ( $MODE eq \\
+"raw_pdb\" || $MODE eq \"raw\")\n{\n while (<$I\
+NFILE>)\n{ print \"$_\";}\n close ( $INFILE);\n\
+ &myexit($EXIT_SUCCESS);\n} \nif ( $MODE eq \
+\"raw4fugue\" )\n{\n while (<$INFILE>)\n{ \n $l\
+=$_;\n if ($l=~/^SEQRES/)\n{\n \n $c= subs\
+tr($l,11,1);\n if ($hc_chain {$c}){print \"$l\\
+";}\n}\n elsif ( $l=~/^ATOM/)\n{\n $c=substr($\
+l,21,1);\n if ($hc_chain {$c}){print \"$l\";}\\
+n}\n}\n close ( $INFILE);\n &myexit($EXIT_SU\
+CCESS);\n} \n\nif ( $MODE eq \"pdb\")\n{\n\n \
+ $read_header=0;\n while (<$INFILE>) \n{\n \
+$line=$_;\n if ($line =~ /^HEADER/){print \\
+"$line\";$read_header=1;}\n}\n close ($INFILE);\
+\n\n if (!$read_header)\n{\n print \"HEADER \
+UNKNOWN 00-JAN-00 \
+ $force_name\\n\";\n}\n\n $INFILE=vfopen ($str\
+ucture_file, \"r\");\n \n print \"COMPND 1\
+ CHAIN:\";\n $last=pop(@c_chain);\n foreach \
+$c ( @c_chain){ print \" $c,\";}\n if ( $last e\
+q \" \"){print \" NULL;\\n\";}\n else \n{\n \
+ print \" $last;\\n\";\n}\n @c_chain=(@c_chain\
+, $last);\n \n print \"REMARK Output of the \
+program extract_from_pdb (Version $VersionTag)\\n\\
+";\n print \"REMARK Legal PDB format not Guaran\
+teed\\n\";\n print \"REMARK This format is not \
+meant to be used in place of the PDB format\\n\";\\
+n print \"REMARK The header refers to the origi\
+nal entry\\n\";\n print \"REMARK The sequence f\
+rom the original file has been taken in the field:\
+ $seq_field\\n\";\n print \"REMARK extract_from\
+_pdb, 2001, 2002, 2003, 2004, 2005 2006 (c) CNRS a\
+nd Cedric Notredame\\n\"; \n if ( $coor_set)\\
+n{\n print \"REMARK Partial chain: Start $st\
+art End $end\\n\";\n}\n if ( $is_nmr)\n{\n \
+ print \"REMARK NMR structure: MODEL $model\\n\";\
+\n}\n \n if ( $n_atom!=0)\n{\n print \"\
+REMARK Contains Coordinates of: \";\n foreac\
+h $a (@atom){print \"$a \";}\n print \"\\n\"\
+;\n} \n}\n\n\n\n\nmy $residue_index = -999;\nmy $\
+old_c = \"TemporaryChain\";\n\nwhile (<$INFILE>) \\
+n{\n $line=$_;\n\n\n if ($line =~ /^SEQRES/)\n{\n\\
+n @field=/(\\S*)\\s*/g;\n\n $c= substr($_,11,1);\
+\n\n \n $l=$#field;\n for ($a=4; $a<$#field ;)\\
+n{\n if (!$onelett{$molecule_type{$c}}->{$field[\
+$a]})\n{\n splice @field, $a, 1;\n}\n else \n\
+{\n $a++;\n}\n}\n \n if ( $c ne $in_chain)\n{\\
+n $pdb_chain_list[$n_pdb_chains]=$c;\n $pdb_ch\
+ain_len [$n_pdb_chains]=$len;\n $in_chain=$c;\n \
+ $n_pdb_chains++;\n}\n \n for ( $a=4; $a<$#field\
+;$a++)\n{\n @{$complete_seq{$c}}->[$complete_seq\
+_len{$c}++]=$field[$a];\n}\n}\n elsif ( $line=~\
+/^ATOM/ || ($line=~/^HETATM/ && &is_aa(substr($lin\
+e,17,3),substr($line,21,1)) && !$no_hetatm))\n{\n\\
+n \n $RAW_AT_ID=$AT_ID=substr($line,12,4);\n $\
+RES_ID=&is_aa(substr($line,17,3),substr($line,21,1\
+));\n $CHAIN=substr($line,21,1);\n\n $RES_NO=su\
+bstr($line,22,4);\n $HOM_CODE=substr ($line, 26, 1\
+);\n $TEMP=substr($line,60,6);\n \n $TEMP=~s/\\s//\
+g;\n $AT_ID=~s/\\s//g;\n $RES_ID=~s/\\s//g;\
+\n $RES_NO=~s/\\s//g;\n \n if ( $HOM_CODE \
+ne $MAIN_HOM_CODE){next;}\n elsif ( $already_read2\
+{$CHAIN}{$RES_ID}{$AT_ID}{$RES_NO}){next;}\n else{\
+$already_read2{$CHAIN}{$RES_ID}{$AT_ID}{$RES_NO}=1\
+;}\n \n \n if ($coor_set && $numbering eq \"file\"\
+ && $residue_index ne $RES_NO)\n{\n \n if \
+( $RES_NO<=$start){$real_start{$CHAIN}++;}\n i\
+f ( $RES_NO<=$end){$real_end{$CHAIN}++;}\n}\n elsi\
+f ($numbering eq \"absolute\")\n{\n $real_star\
+t{$CHAIN}=$start;\n $real_end{$CHAIN}=$end;\n}\
+\n\n $KEY=\"ALL\";\n if ( $CHAIN ne \
+$in_atom_chain)\n{\n \n $pdb_atom_chain_list\
+[$n_pdb_atom_chains]=$c;\n $pdb_atom_chain_len [\
+$n_pdb_atom_chains]=$len;\n $in_atom_chain=$c;\n\
+ $n_pdb_atom_chains++;\n}\n \n if ( $residue_ind\
+ex ne $RES_NO)\n{\n $residue_index = $RES_NO;\
+\n @{$atom_seq{$CHAIN}}->[$atom_seq_len{$CHAI\
+N}++]=$RES_ID;;\n}\n}\n\n}\nclose ($INFILE);\n\n\n\
+\n\n\n\n$INFILE=vfopen ($structure_file, \"r\");\n\
+foreach $c (@c_chain)\n{\n\n if ( $seq_field eq\
+ \"SEQRES\"){@pdb_seq=@{$complete_seq{$c}};}\n els\
+if ( $seq_field eq \"ATOM\") {@pdb_seq=@{$atom_se\
+q{$c}};}\n \n\n $full_length=$l=$#pdb_seq+1;\n \n\
+ if ( $real_end{$c}==\"*\"){$real_end{$c}=$full_le\
+ngth;}\n if ( $coor_set)\n{ \n\n if ( $real_\
+end{$c} < $l){splice @pdb_seq, $real_end{$c}, $l;}\
+\n if ( $real_start{$c} < $l){splice @pdb_seq, \
+0, $real_start{$c}-1;} \n $l=$#pdb_seq;\n\
+}\n\n elsif ( $delete_set)\n{\n splice @pdb_seq\
+, $delete_start, $delete_end-$delete_start+1;\n \
+ $l=$#pdb_seq;\n}\n \n $new_fasta_name=\"$pdb_id$c\
+\";\n if ( $coor_set)\n{\n if ( $n_pdb_chains==\
+0){$new_fasta_name=\"$new_fasta_name$c\";}\n $n\
+ew_fasta_name= $new_fasta_name.\"\\_$start\\_$end\\
+";\n}\n \n if ( $MODE eq \"pdb\")\n{\n $nl=1\
+;\n $n=0;\n \n foreach $res ( @pdb_seq)\n\
+ {\n if ( !$n)\n {\n \n printf \"SEQRES %3d \
+%1s %4d \", $nl,$c, $l;\n $nl++;\n }\n $re\
+s=~s/\\s//g;\n \n if ($code==1){ printf \
+\"%3s \",$onelett{$molecule_type{$c}}->{$res};}\n \
+ elsif ($code==3){ printf \"%3s \",$res};\n \
+ \n $n++; \n if ( $n==13){$n=0;pri\
+nt \"\\n\";}\n}\n if ( $n!=0){print \"\\n\"; $n=\
+0;}\n}\n elsif ( $MODE eq \"simple\")\n{\n print\
+ \"# SIMPLE_PDB_FORMAT\\n\";\n if ( $new_fasta_n\
+ame eq \" \"){$new_fasta_name=\"dummy_name\";}\n \
+ print \">$new_fasta_name\\n\";\n\n foreach $res\
+ ( @pdb_seq)\n{\n print \"$onelett{$molecule\
+_type{$c}}->{$res}\";\n}\n print \"\\n\";\n}\n e\
+lsif ( $MODE eq \"fasta\")\n{\n $n=0;\n print \
+\">$new_fasta_name\\n\";\n \n foreach $res ( @\
+pdb_seq)\n{\n\n print \"$onelett{$molecule_t\
+ype{$c}}->{$res}\";\n $n++;\n i\
+f ( $n==60){print \"\\n\"; $n=0;}\n}\n print \"\\
+\n\"; \n}\n}\n\nif ( $MODE eq \"fasta\")\n{\n \
+&myexit($EXIT_SUCCESS);\n \n}\n\n \n $charcount\
+=0;\n $inchain=\"BEGIN\";\n $n=0;\n while (<$IN\
+FILE>) \n{\n $line=$_;\n \n if ($line =~\
+/^ATOM/ || ($line=~/^HETATM/))\n{\n $line_header\
+=\"UNKNWN\";\n $RES_ID=substr($line,17,3);\n $chai\
+n = substr($line,21,1);\n\n if ($line =~/^ATOM/)\n\
+{\n $line_header=\"ATOM\";\n $RES_ID=(&is_\
+aa($RES_ID,$chain))?&is_aa($RES_ID,$chain):$RES_ID\
+;\n}\n elsif ($line=~/^HETATM/ && ($ligand_list {$\
+RES_ID} ||$ligand_list {'ALL'} || !&is_aa($RES_ID,\
+$chain)))\n{\n $line_header=\"HETATM\";\n}\n e\
+lsif ($line=~/^HETATM/ && (&is_aa($RES_ID,$chain) \
+&& !$no_hetatm))\n{\n $line_header=\"ATOM\";\n\
+ $RES_ID=&is_aa($RES_ID,$chain);\n}\n else\n{\\
+n next;\n}\n\n \n\n $X=substr($line,30,8); \
+ \n $Y=substr($line,38,8);\n $Z=substr($line,46,8)\
+;\n $TEMP=substr($line,60,6);\n \n $RAW_AT_ID=$AT_\
+ID=substr($line,12,4);\n $CHAIN=substr($line,21,1)\
+;\n $RES_NO=substr($line,22,4);\n $HOM_CODE=substr\
+ ($line, 26, 1);\n \n $X=~s/\\s//g;\n $Y=~s/\\s//g\
+;\n $Z=~s/\\s//g;\n $TEMP=~s/\\s//g;\n \n $AT_ID=~\
+s/\\s//g;\n $RES_ID=~s/\\s//g;\n $RES_NO=~s/\\s//g\
+;\n\n \n if ( $HOM_CODE ne $MAIN_HOM_CODE){next;}\\
+n elsif ( $already_read{$CHAIN}{$RES_ID}{$AT_ID}{$\
+RES_NO}){next;}\n else{$already_read{$CHAIN}{$RES_\
+ID}{$AT_ID}{$RES_NO}=1;}\n \n $KEY=\"ALL\";\n\n \
+ if ( $RES_NO ==0){$start_at_zero=1;}\n\n $RES_\
+NO+=$start_at_zero; \n \n if ( $current_chain n\
+e $CHAIN)\n{\n $current_chain=$CHAIN;\n $p\
+os=$current_residue=0;\n $offset=($coor_set)?(\
+$real_start{$CHAIN}-1):0;\n if ( $seq_field\
+ eq \"SEQRES\"){@ref_seq=@{$complete_seq{$CHAIN}};\
+}\n elsif ( $seq_field eq \"ATOM\") {@ref_seq\
+=@{$atom_seq{$CHAIN}};}\n}\n \n if ($current_resid\
+ue != $RES_NO)\n{\n $current_residue=$RES_NO;\\
+n if ( $seq_field eq \"SEQRES\"){$pos=$curr\
+ent_residue;}\n elsif ( $seq_field eq \"ATOM\"\
+){$pos++;}\n}\n \n \n if ($n_atom==0 || $atom_list\
+{$AT_ID}==1 || $atom_list{$KEY}==1)\n{ \n \n \
+ $do_it=(!@c_chain || $hc_chain{$CHAIN} ||$hc_c\
+hain{'LIGAND'} );\n \n $do_it= ($do_it==1)\
+ && ($coor_set==0 ||($pos>=$real_start{$CHAIN} && \
+$pos<=$real_end{$CHAIN}));\n $do_it= ($do_it==\
+1) && ($delete_set==0 || $pos<$delete_start ||$pos\
+>$delete_end );\n if ($ligand==0 && $line_head\
+er eq \"HETATM\" ){$do_it=0;}\n if ($ligand_on\
+ly==1 && $line_header eq \"ATOM\" ){$do_it=0;}\n \
+ if ($ligand==1 && $line_header eq \"HETATM\" &&\
+ $ligand_list{$RES_ID}==0 && $ligand_list{\"ALL\"}\
+==0){$do_it=0;} \n \n \n if ( $do_it)\\
+n{\n $n++;\n $out_pos=$pos;\n \n if ( $d\
+elete_set)\n{\n if ( $out_pos< $delete_start){;\
+}\n else {$offset=$delete_end-$delete_start;}\n\
+} \n \n if ( $numbering_out eq\
+ \"new\"){$out_pos-=$offset;}\n elsif ( $nu\
+mbering_out eq \"old\"){$out_pos=$RES_NO;}\n \
+ \n \n \n if ( $code==1){$RES\
+_ID=$onelett{$molecule_type{$c}}->{$RES_ID};}\n \
+ \n if ($unfold)\n{\n $unfolded_x+=5;\\
+n $X=$unfolded_x;\n $Y=0;\n $Z=0;\n \
+ $float=1;\n}\n else\n{\n $float=3;\n}\
+\n\n if ( $MODE eq \"pdb\")\n{\n printf\
+ \"%-6s%5d %-4s %3s %s%4d %8.3f%8.3f%8.3f 1.00\
+ %5.2f\\n\",$line_header, $n, $RAW_AT_ID,$RES_ID,$\
+CHAIN,$out_pos, $X, $Y, $Z,$TEMP; \n}\n \
+elsif ( $MODE eq \"simple\")\n{\n if ( $RES_I\
+D eq \"\"){$RES_ID=\"X\";}\n printf \"%-6s %5s \
+%s %2s %4d %8.3f %8.3f %8.3f\\n\",$line_header,\
+ $AT_ID, $RES_ID,($CHAIN eq\"\" || $CHAIN eq \" \"\
+)?\"A\":$CHAIN,$out_pos, $X, $Y, $Z,$TEMP;\n}\n\n}\
+\n}\n}\n}\nprint \"\\n\";\nclose($INFILE);\n\n\nif\
+ ( $error ne \"\") \n{$error=$error.\"\\nDiagnosti\
+c: SEQRES and the residues in ATOM are probably\
+ Incompatible\\n\";\n $error=$error. \"Recomen\
+dation: Rerun with '-fix 1' in order to ignore the\
+ SEQRES sequences\\n\";\n}\nif (!$nodiagnostic){pr\
+int STDERR $error;}\n&myexit ( $EXIT_SUCCESS);\n\n\
+sub is_released \n {\n my ($r);\n my $in=@_\
+[0];\n my $name=&remote_is_pdb_name ($in);\n \
+ my $hold=&remote_is_on_hold($in);\n \n $r=(\
+$name && !$hold)?1:0;\n return $r;\n }\nsub re\
+mote_is_pdb_name \n{\n my $in=@_[0];\n my ($\
+ref_file, $pdb);\n my ($value,$value1,$value2);\
+\n\n if ( $in=~/[^\\w\\d\\:\\_]/){return 0;}\n \
+ $ref_file=\"$cache/pdb_entry_type.txt\";\n \\
+n if ( !-e $ref_file || (-M $ref_file)>2 || -z \
+$ref_file)\n {\n &url2file(\"ftp://ftp.wwpdb.\
+org/pub/pdb/derived_data/pdb_entry_type.txt\", $re\
+f_file);\n }\n $pdb=substr ($in,0, 4);\n \
+ chomp(($value1=`grep -c $pdb $ref_file`));\n \
+$pdb=lc($pdb);\n chomp(($value2=`grep -c $pdb $\
+ref_file`));\n $value=($value1 || $value2)?1:0;\
+\n $value=($value>0)?1:0;\n \n return $va\
+lue;\n }\n\nsub pdb2model_type\n{\n my $in=@_[\
+0];\n my ($ref_file, $pdb);\n my ($value, $r\
+et);\n\n if ( $in=~/[^\\w\\d\\:\\_]/){return 0;\
+}\n $ref_file=\"$cache/pdb_entry_type.txt\";\n \
+ \n if ( !-e $ref_file || (-M $ref_file)>2 ||\
+ -z $ref_file)\n {\n &url2file(\"ftp://ftp.ww\
+pdb.org/pub/pdb/derived_data/pdb_entry_type.txt\",\
+ $ref_file);\n }\n $pdb=substr ($in,0, 4);\
+\n $pdb=lc($pdb);\n \n chomp(($value=`gre\
+p $pdb $ref_file`));\n \n $value=~/^\\S+\\s+\
+\\S+\\s+(\\S+)/;\n $ret=$1;\n if ( $ret eq\"\
+\"){return \"UNKNOWN\";}\n \n return $ret;\n\
+ }\nsub remote_is_on_hold\n {\n my $in=@_[0];\
+\n my ($ref_file, $pdb);\n my ($value1, $val\
+ue2,$value);\n \n if ( $in=~/[^\\w\\d\\:\\_]\
+/){return 0;}\n $ref_file=\"$cache/unreleased.x\
+ml\";\n \n if ( !-e $ref_file || (-M $ref_fi\
+le)>2 || -z $ref_file)\n {\n &url2file(\"http\
+://www.rcsb.org/pdb/rest/getUnreleased\",$ref_file\
+);\n }\n \n $pdb=substr ($in,0, 4);\n \
+ chomp(($value1=`grep -c $pdb $ref_file`));\n \
+$pdb=lc($pdb);\n chomp(($value2=`grep -c $pdb $\
+ref_file`));\n $value=($value1 || $value2)?1:0;\
+\n $value=($value>0)?1:0;\n return $value;\n\
+ }\nsub is_pdb_file\n{\n my @arg=@_;\n\n if\
+ ( !-e $arg[0]){return 0;}\n \n $F=vfopen ($\
+arg[0], \"r\");\n while ( <$F>)\n{\n if (/^HEAD\
+ER/)\n{\n close $F;\n return 1;\n}\n elsif\
+ ( /^SEQRES/)\n{\n close $F;\n return 1;\n\
+}\n elsif ( /^ATOM/)\n{\n close $F;\n retu\
+rn 1;\n}\n}\n return 0;\n}\nsub get_pdb_id\n{\n\
+ my $header_file=@_[0];\n my $id;\n my $F\
+= new FileHandle;\n \n \n $F=vfopen (\"$h\
+eader_file\", \"r\");\n\n while ( <$F>)\n \
+{\n if ( /HEADER/)\n {\n if ($debug){print \\
+"$_\";}\n $id=substr($_,62,4 );\n return $\
+id;\n }\n }\n close ($F);\n \n ret\
+urn \"\";\n}\n\nsub get_ligand_list\n{\n my $pd\
+b_file=@_[0];\n my $chain;\n my $ligand;\n \
+ my %complete_ligand_list;\n \n\n $F=vfopen\
+ ($pdb_file, \"r\");\n while ( <$F>)\n{\n if ( \
+/^HETATM/)\n{\n $line=$_;\n $chain=substr(\
+$line,21,1);\n $ligand=substr($line,17,3);\n \
+ \n if (!$complete_ligand_list{$chain}{$liga\
+nd})\n{\n \n $complete_ligand_list{\"result\"}.=\
+\"CHAIN $chain LIGAND $ligand\\n\";\n $complete_l\
+igand_list{$chain}{$ligand}=1;\n}\n}\n}\n close\
+ ($F);\n return %complete_ligand_list;\n}\n\nsu\
+b get_chain_list \n{\n my $header_file;\n my\
+ @chain_list;\n my @list;\n my $n_chains;\n \
+ my %chain_hasch;\n my $pdb_file=@_[0];\n \
+my $c;\n my %hasch;\n my $chain;\n \n \n\
+ $F=vfopen ($pdb_file, \"r\");\n while ( <$F\
+>)\n{\n\n\n if (/SEQRES\\s+\\d+\\s+(\\S+)/)\n {\\
+n $chain = substr($_,11,1);$chain=~s/\\s//g;if\
+ ( $chain eq \"\"){$chain=\" \";}\n if (!$hasc\
+h{$chain}){$hasch{$chain}=1;push @chain_list, $cha\
+in;}\n }\n if (/^ATOM/ || /^HETATM/)\n {\n \
+ $chain = substr($_,21,1); $chain=~s/\\s//g;if ( $\
+chain eq \"\"){$chain=\" \";}\n if (!$hasch{$c\
+hain}){$hasch{$chain}=1;push @chain_list, $chain;}\
+\n }\n }\n\n\nclose ($F);\nif (!@chain_list\
+)\n {\n @chain_list=(\"A\");\n }\n\n\nreturn \
+@chain_list;\n}\n\nsub token_is_in_list\n{\n\n \
+my @list=@_;\n my $a;\n \n for ($a=1; $a<\
+=$#list; $a++)\n{\n if ( $list[$a] eq $list[0]){re\
+turn $a;}\n}\n}\n\nsub pdb_name2name_and_chain \n{\
+\n my $pdb_file=@_[0];\n my $pdb_file_in;\n \
+ my @array;\n my $chain;\n my $c;\n\n $\
+pdb_file_in=$pdb_file;\n\n $pdb_file=~/^(.{4})/\
+;$pdb_id=$1;\n @array=($pdb_file=~/([\\w])/g);\\
+n \n \n $chain=uc ($array[4]);\n $chain=($\
+chain eq \"\")?\"FIRST\":$chain;\n \n return\
+ ( $pdb_id, $chain);\n\n if ( $#array==3){retur\
+n ($pdb_id, \"FIRST\");}\n elsif ( $#array<4){ \
+return ($pdb_id, \"\");}\n else {return ( $pdb_\
+id, $chain);}\n \n \n \n}\nsub get_main\
+_hom_code \n{\n my $pdb_file=@_[0];\n my %ho\
+m, $n, $best, $best_h;\n open (F, $pdb_file);\n\
+ while (<F>)\n{\n if ( $_=~/^ATOM/)\n{\n $h\
+=substr ($_,26, 1);\n $n=++$hom{$h};\n if \
+($n>$best)\n{\n $best=$n;\n $best_h=$h;\n}\n}\n}\
+\n close (F);\n return $best_h;\n}\n\n\nsub \
+get_pdb_file \n{\n my ($pdb_file_in)=(@_);\n \
+ my $result;\n my @letter;\n my @chain;\n \
+ my $v;\n my $pdb_file=$pdb_file_in;\n\n $pd\
+b_file=($pdb_file_in=~/\\S+_S_(\\S+)/)?$1:$pdb_fil\
+e_in;\n \n if ($no_remote_pdb_dir==0)\n \
+ {\n $no_remote_pdb_dir=1;\n $result=get_pdb_file3\
+ ($pdb_file);\n $no_remote_pdb_dir=0;\n if ( $resu\
+lt){return $result;}\n else\n {\n \n lc \
+($pdb_file);\n $result=get_pdb_file3($pdb_file\
+);\n return $result;\n }\n }\n else\
+\n {\n return get_pdb_file3 ($pdb_file);\n \
+ }\n \n }\n\nsub get_pdb_file3 \n{\n my $\
+pdb_file_in=@_[0];\n my $result;\n my @lette\
+r;\n my @chain;\n my $lcfile;\n my $ucfil\
+e;\n my $pdb_file=$pdb_file_in;\n \n $lcf\
+ile=lc $pdb_file;\n $ucfile=uc $pdb_file;\n\n \
+ if ( ($result=get_pdb_file2 ($pdb_file))){return\
+ $result;}\n \n\n if ($lcfile ne $pdb_file &\
+& ($result=get_pdb_file2 ($lcfile))){return $resul\
+t;}\n if ($ucfile ne $pdb_file && ($result=get_\
+pdb_file2 ($ucfile))){return $result;}\n \n \\
+n \n return \"\";\n}\nsub get_pdb_file2\n{\n\
+ my $pdb_file=@_[0];\n my $return_value;\n \
+ \n $return_value=\"\";\n \n if ( ($resu\
+lt=get_pdb_file1 ($pdb_file))){$return_value=$resu\
+lt;}\n elsif ( !($pdb_file=~/\\.pdb/) && !($pdb\
+_file=~/\\.PDB/))\n{\n if ( ($result=get_pdb_file1\
+ (\"$pdb_file.pdb\"))){$return_value=$result;}\n e\
+lsif ( ($result=get_pdb_file1 (\"$pdb_file.PDB\"))\
+){$return_value=$result;}\n\n elsif ( ($result=get\
+_pdb_file1 (\"pdb$pdb_file.pdb\"))){$return_value=\
+$result;} \n elsif ( ($result=get_pdb_file1 (\"pdb\
+$pdb_file.PDB\"))){$return_value=$result;}\n elsif\
+ ( ($result=get_pdb_file1 (\"PDB$pdb_file.PDB\")))\
+{$return_value=$result;}\n elsif ( ($result=get_pd\
+b_file1 (\"PDB$pdb_file.pdb\"))){$return_value=$re\
+sult;}\n \n \n elsif ( ($result=get_pdb_file1 (\"$\
+pdb_file.ent\"))){$return_value=$result;}\n elsif \
+( ($result=get_pdb_file1 (\"pdb$pdb_file.ent\"))){\
+$return_value=$result;}\n elsif ( ($result=get_pdb\
+_file1 (\"PDB$pdb_file.ent\"))){$return_value=$res\
+ult;}\n\n elsif ( ($result=get_pdb_file1 (\"$pdb_f\
+ile.ENT\"))){$return_value=$result;}\n elsif ( ($r\
+esult=get_pdb_file1 (\"pdb$pdb_file.ENT\"))){$retu\
+rn_value=$result;}\n elsif ( ($result=get_pdb_file\
+1 (\"PDB$pdb_file.ENT\"))){$return_value=$result;}\
+\n \n \n \n}\n return $return_value;\n}\n \n\
+sub get_pdb_file1\n{\n my ($pdb_file)=(@_);\n \
+ my $return_value;\n \n\n $return_value=\"\\
+";\n if ( ($result=get_pdb_file0 ($pdb_file))){\
+$return_value=$result;}\n elsif ( ($result=get_\
+pdb_file0 (\"$pdb_file.Z\"))){$return_value=$resul\
+t;}\n elsif ( ($result=get_pdb_file0 (\"$pdb_fi\
+le.gz\"))){$return_value=$result;}\n elsif ( ($\
+result=get_pdb_file0 (\"$pdb_file.GZ\"))){$return_\
+value=$result;}\n return $return_value;\n}\nsub\
+ get_pdb_file0 \n{ \n my ($pdb_file, $attempt)=\
+(@_);\n my $pdb_file=@_[0];\n my $tmp_pdb_fi\
+le; \n my $return_value;\n\n if ( !$attem\
+pt){$attempt=1;}\n \n $local_pdb_file=\"$pdb\
+_file\";\n if ( $local_pdb_file eq \"\")\n{\n $\
+tmp_pdb_file=vtmpnam();\n open F, \">$tmp_pdb_file\
+\";\n \n while (<STDIN>){print F \"$_\";}\n close \
+(F);\n \n if (-e $tmp_pdb_file && &is_pdb_file ( $\
+local_pdb_file))\n{return $tmp_pdb_file;}\n}\n\n \
+ $local_pdb_file=\"$pdb_file\";\n &debug_print\
+ (\"\\nTry access local file: $local_pdb_file\");\\
+n \n $local_pdb_file=&check_pdb_file4compres\
+sion ($local_pdb_file);\n if ( -e $local_pdb_fi\
+le && (&is_pdb_file ($local_pdb_file) || $force_pd\
+b))\n{\n &debug_print ( \"\\n\\tIs in Current Dir\\
+");\n $tmp_pdb_file=vtmpnam();\n `cp $local_pdb_fi\
+le $tmp_pdb_file`;\n return $tmp_pdb_file;\n}\n \
+ else\n{\n &debug_print (\"\\n\\tFile Not in Curre\
+nt Dir\");\n}\n\n if ($pdb_file=~/^pdb/||$pdb_f\
+ile=~/^PDB/){$pdb_div=substr ($pdb_file, 4, 2);}\n\
+ else\n{\n $pdb_div=substr ($pdb_file, 1, 2);\
+\n}\n $local_pdb_file=\"$pdb_dir/$pdb_div/$pdb_\
+file\";\n $local_pdb_file=&check_pdb_file4compr\
+ession ( $local_pdb_file);\n &debug_print (\"\\\
+nTry access file From PDB_DIR: $local_pdb_file\");\
+\n if ($pdb_dir && -e $local_pdb_file && &is_pd\
+b_file ($local_pdb_file))\n{\n &debug_print ( \"\\\
+n\\tIs in Local PDB DIR\");\n $tmp_pdb_file=vtmpna\
+m();\n `cp $local_pdb_file $tmp_pdb_file`;\n retur\
+n $tmp_pdb_file;\n}\n\n $local_pdb_file=\"$pdb_\
+dir/$pdb_file\";\n $local_pdb_file=&check_pdb_f\
+ile4compression ( $local_pdb_file);\n &debug_pr\
+int (\"\\nTry access file From PDB_DIR: local_pdb_\
+file\");\n if ($pdb_dir && -e $local_pdb_file &\
+& &is_pdb_file ($local_pdb_file))\n{\n &debug_prin\
+t ( \"\\n\\tIs in Local PDB DIR\");\n $tmp_pdb_fil\
+e=vtmpnam();\n `cp $local_pdb_file $tmp_pdb_file`;\
+\n return $tmp_pdb_file;\n}\n\n $local_pdb_file\
+=\"$pdb_dir$pdb_file\";\n $local_pdb_file=&chec\
+k_pdb_file4compression ( $local_pdb_file);\n &d\
+ebug_print (\"\\nTry access file From PDB_DIR: $lo\
+cal_pdb_file\");\n if ($pdb_dir && -e $local_pd\
+b_file && &is_pdb_file ($local_pdb_file))\n{\n &de\
+bug_print ( \"\\n\\tIs in Local PDB DIR\");\n $tmp\
+_pdb_file=vtmpnam();\n `cp $local_pdb_file $tmp_pd\
+b_file`;\n return $tmp_pdb_file;\n}\n else\n{&d\
+ebug_print ( \"\\n\\tNot In Local Pdb Dir\");}\n\n\
+ if ($cache ne \"NO\" && $cache ne \"no\")\n{\n\
+\n $local_pdb_file=\"$cache/$pdb_file\";\n $local_\
+pdb_file=&check_pdb_file4compression ( $local_pdb_\
+file);\n &debug_print(\"\\nTry access file From Ca\
+che: $local_pdb_file\");\n if (-e $local_pdb_file \
+&& &is_pdb_file ($local_pdb_file))\n{\n &debug\
+_print ( \"\\n\\tIs in T-Coffee Cache\");\n $t\
+mp_pdb_file=vtmpnam();\n `cp $local_pdb_file $\
+tmp_pdb_file`;\n return $tmp_pdb_file;\n}\n el\
+se{&debug_print ( \"\\n\\tNot in Cache Dir\");}\n}\
+\n\nif (!$no_remote_pdb_dir) \n {\n my $value=\
+&is_released ($pdb_file);\n my $return_value=\"\
+\";\n if ($value==1)\n {\n \n &debug_print\
+ (\"\\n*******************************************\
+**********\\nTry Remote Access for $pdb_file\");\n\
+ $tmp_pdb_file=vtmpnam();\n $netcommand=$netaddres\
+s;\n $netcommand=~s/%%/$pdb_file/g;\n &url2file(\"\
+$netcommand\", \"$tmp_pdb_file.$netcompression\");\
+\n &debug_print(\"\\nREMOTE: $netcommand\\n\");\n \
+\n $compressed_tmp_file_name=\"$tmp_pdb_file.$netc\
+ompression\";\n \n if ($netcompression && -B $comp\
+ressed_tmp_file_name)\n {\n my $r;\n &de\
+bug_print (\"\\n\\tFile Found Remotely\");\n i\
+f (($r=safe_system ( \"$netcompression_pg $compres\
+sed_tmp_file_name\")!=$EXIT_SUCCESS) && $attempts<\
+5)\n {\n &debug_print (\"\\n\\tProper Downl\
+oad Failed Try again\");\n unlink $compressed_tmp\
+_file_name;\n print \"\\nFailed to Download $comp\
+ressed_tmp_file_name. New Attempt $attempt/5\\n\";\
+\n return &get_pdb_file0($pdb_file, $attempt+1);\\
+n }\n elsif ($r== $EXIT_SUCCESS)\n \
+ {\n &debug_print (\"\\n\\tProper Download Succee\
+ded \");\n $return_value=$tmp_pdb_file;\n }\
+\n else\n {\n &debug_print (\"\\n\\tPro\
+per Download Failed \");\n &debug_print (\"\\nFil\
+e Not Found Remotely\");\n unlink $compressed_tmp\
+_file_name;\n }\n }\n else\n {\n\n &\
+debug_print (\"\\nFile Not Found Remotely\");\n \
+ unlink $compressed_tmp_file_name;\n }\n #Updat\
+e cache if required\n if ($cache ne \"no\" && $cac\
+he ne \"update\" && -e $return_value)\n {\n \
+`cp $return_value $cache/$pdb_file.pdb`;\n #`t\
+_coffee -other_pg clean_cache.pl -file $pdb_file.p\
+db -dir $cache`;\n }\n }\n &debug_print \
+(\"\\nRemote Download Finished\");\n return $re\
+turn_value;\n }\nreturn \"\";\n}\n\nsub check_pdb\
+_file4compression \n{\n my $file=@_[0];\n my\
+ $tmp;\n my $r;\n \n $tmp=&vtmpnam();\n \
+ if (-e $tmp){unlink $tmp;}\n \n $file=~s/\\
+\/\\//\\//g;\n if (-B $file && ($file=~/\\.Z\
+/)) {`cp $file $tmp.Z`;`rm $tmp`;`gunzip $tmp.Z $S\
+ILENT`;$r=$tmp;}\n elsif (-B $file && ($file=~/\
+\\.gz/)){`cp $file $tmp.gz`;`gunzip $tmp.gz $SILEN\
+T`;return $r=$tmp;}\n elsif (-B $file ){`cp $fi\
+le $tmp.gz`;`gunzip $tmp.gz $SILENT`;$r=$tmp;}\n \
+ elsif ( -e $file ) {$r= $file;}\n elsif ( -e \
+\"$file.gz\" ){ `cp $file.gz $tmp.gz`;`gunzip \
+$tmp.gz $SILENT`;$r=$tmp;} \n elsif ( -e \"$\
+file.Z\") {`cp $file.Z $tmp.Z`; `gunzip $tmp.Z $S\
+ILENT`;$r=$tmp;}\n else {$r= $file;}\n\n if\
+ ( -e \"$tmp.Z\"){unlink \"$tmp.Z\";}\n if ( -e\
+ \"$tmp.gz\"){unlink \"$tmp.gz\";}\n \n retu\
+rn $r;\n \n}\n\n\n\n\n\n \n\n\n\n\n\n\n\nsub\
+ vfopen \n{\n my $file=@_[0];\n my $mode=@_[\
+1];\n my $tmp;\n my $F = new FileHandle;\n \
+ \n \n $tmp=$file;\n \n \n if ( $mode\
+ eq \"r\" && !-e $file){ myexit(flush_error (\"Can\
+not open file $file\"));}\n elsif ($mode eq \"w\
+\"){$tmp=\">$file\";}\n elsif ($mode eq \"a\"){\
+$tmp=\">>$file\";}\n \n \n open ($F,$tmp)\
+;\n return $F;\n}\nsub debug_print\n{\n my $\
+message =@_[0];\n if ($debug){print STDERR \"NO\
+_REMOTE_PDB_DIR: $no_remote_pdb_dir - $message [DE\
+BUG:extract_from_pdb]\";}\n return;\n}\nsub is_\
+aa \n{\n my ($aa, $chain) =@_;\n\n my $one;\\
+n my $trhee;\n \n if ( $onelett{$molecule\
+_type{$chain}}->{$aa} eq 'X' || !$onelett{$molecul\
+e_type{$chain}}->{$aa} ){return '';}\n else\n \
+ {\n $one=$onelett{$molecule_type{$chain}}->{$a\
+a};\n\n $three=$threelett{$molecule_type{$chain}}-\
+>{$one};\n \n\n return $three;\n }\n }\n\n\n\
+\n\n\nsub url2file\n{\n my ($address, $out, $wg\
+et_arg, $curl_arg)=(@_);\n my ($pg, $flag, $r, \
+$arg, $count);\n \n if (!$CONFIGURATION){&ch\
+eck_configuration (\"wget\", \"INTERNET\", \"gzip\\
+");$CONFIGURATION=1;}\n \n if (&pg_is_instal\
+led (\"wget\")) {$pg=\"wget\"; $flag=\"-O\";$arg\
+=$wget_arg;}\n elsif (&pg_is_installed (\"curl\\
+")){$pg=\"curl\"; $flag=\"-o\";$arg=$curl_arg;}\n \
+ return safe_system (\"$pg $flag$out $address >/\
+dev/null 2>/dev/null\");\n\n}\n\n\n\n\nsub pdbfile\
+2chaintype\n {\n my $file=@_[0];\n my %ct;\\
+n my $F;\n \n $F=vfopen ($file, \"r\");\n\
+ while (<$F>)\n {\n my $line=$_;\n if ($li\
+ne =~/^ATOM/)\n {\n my $C=substr($line,21,1)\
+;\n if (!$ct{$C})\n { \n my $r=substr($\
+line,17,3);\n $r=~s/\\s+//;\n if (length ($r)==1\
+){$ct{$C}=\"R\";}\n elsif (length ($r)==2){$ct{$C\
+}=\"D\";}\n elsif (length ($r)==3){$ct{$C}=\"P\";\
+}\n else \n {\n myexit(flush_error(\"ERRO\
+R: Could not read RES_ID field in file $file\"));\\
+n }\n }\n }\n }\n close ($F);\n\
+ return %ct;\n }\n \n \n\n\n\nsub fill_th\
+reelett_RNA\n{\n\n my %threelett=(\n 'A', ' A',\n\
+ 'T', ' T',\n 'U', ' U',\n 'C', ' C',\n 'G', ' \
+ G',\n 'I', ' I', #Inosine\n );\n \n return %thre\
+elett;\n\n}\n\n\nsub fill_onelett_RNA\n{\n my %o\
+nelett=(\n ' A' => 'A',\n ' T' => 'T',\n ' U' =\
+> 'U',\n ' C' => 'C',\n ' G' => 'G',\n 'CSL' => \
+'X',\n 'UMS' => 'X',\n ' I' => 'I',\n 'A' => 'A',\
+\n 'T' => 'T',\n 'U' => 'U',\n 'C' => 'C',\n 'G' =\
+> 'G',\n 'I' => 'I',\n );\n\n return %onelett;\n\n\
+}\n\n\nsub fill_onelett_DNA\n{\n my %onelett=(\n\
+ ' DA', 'A',\n ' DT', 'T',\n ' DC', 'C',\n ' DG', \
+'G',\n 'DA', 'A',\n 'DT', 'T',\n 'DC', 'C',\n 'DG'\
+, 'G',\n );\n\n return %onelett;\n\n}\n\nsub fill_\
+threelett_DNA\n{\n\n my %threelett=(\n 'A', ' DA',\
+\n 'T', ' DT',\n 'C', ' DC',\n 'G', ' DG',\n );\n\\
+n return %threelett;\n\n}\n\n\n\n\nsub fill_threel\
+ett_prot\n{ \n my %threelett;\n\n %threelett=(\\
+n'A', 'ALA',\n'C', 'CYS',\n'D', 'ASP',\n'E', 'GLU'\
+,\n'F', 'PHE',\n'G', 'GLY',\n'H', 'HIS',\n'I', 'IL\
+E',\n'K', 'LYS',\n'L', 'LEU',\n'N', 'ASN',\n'M', '\
+MET',\n'P', 'PRO',\n'Q', 'GLN',\n'R', 'ARG',\n'S',\
+ 'SER',\n'T', 'THR',\n'V', 'VAL',\n'W', 'TRP',\n'Y\
+', 'TYR',\n);\n\nreturn %threelett;\n\n\n}\n\nsub \
+fill_onelett_prot\n{\n my %onelett;\n \n \
+%onelett=(\n\n'10A', 'X',\n'11O', 'X',\n'12A', 'X'\
+,\n'13P', 'X',\n'13R', 'X',\n'13S', 'X',\n'14W', '\
+X',\n'15P', 'X',\n'16A', 'X',\n'16G', 'X',\n'1AN',\
+ 'X',\n'1AP', 'X',\n'1AR', 'X',\n'1BH', 'X',\n'1BO\
+', 'X',\n'1C5', 'X',\n'1CU', 'X',\n'1DA', 'X',\n'1\
+GL', 'X',\n'1GN', 'X',\n'1IN', 'X',\n'1LU', 'L',\n\
+'1MA', 'X',\n'1MC', 'X',\n'1MG', 'X',\n'1MZ', 'X',\
+\n'1NA', 'X',\n'1NB', 'X',\n'1NI', 'X',\n'1PA', 'A\
+',\n'1PC', 'X',\n'1PE', 'X',\n'1PG', 'X',\n'1PI', \
+'A',\n'1PM', 'X',\n'1PN', 'X',\n'1PU', 'X',\n'1PY'\
+, 'X',\n'1UN', 'X',\n'24T', 'X',\n'25T', 'X',\n'26\
+P', 'X',\n'2AB', 'X',\n'2AM', 'X',\n'2AN', 'X',\n'\
+2AP', 'X',\n'2AR', 'X',\n'2AS', 'D',\n'2BL', 'X',\\
+n'2BM', 'X',\n'2CP', 'X',\n'2DA', 'X',\n'2DG', 'X'\
+,\n'2DP', 'X',\n'2DT', 'X',\n'2EP', 'X',\n'2EZ', '\
+X',\n'2FG', 'X',\n'2FL', 'X',\n'2FP', 'X',\n'2FU',\
+ 'X',\n'2GL', 'X',\n'2GP', 'X',\n'2HP', 'X',\n'2IB\
+', 'X',\n'2IP', 'X',\n'2LU', 'L',\n'2MA', 'X',\n'2\
+MD', 'X',\n'2ME', 'X',\n'2MG', 'X',\n'2ML', 'L',\n\
+'2MO', 'X',\n'2MR', 'R',\n'2MU', 'X',\n'2MZ', 'X',\
+\n'2NO', 'X',\n'2NP', 'X',\n'2OG', 'X',\n'2PA', 'X\
+',\n'2PC', 'X',\n'2PE', 'X',\n'2PG', 'X',\n'2PH', \
+'X',\n'2PI', 'X',\n'2PL', 'X',\n'2PP', 'X',\n'2PU'\
+, 'X',\n'2SI', 'X',\n'2TB', 'X',\n'34C', 'X',\n'35\
+G', 'X',\n'3AA', 'X',\n'3AD', 'X',\n'3AH', 'H',\n'\
+3AN', 'X',\n'3AP', 'X',\n'3AT', 'X',\n'3BT', 'X',\\
+n'3CH', 'X',\n'3CN', 'X',\n'3CO', 'X',\n'3CP', 'X'\
+,\n'3DR', 'X',\n'3EP', 'X',\n'3FM', 'X',\n'3GA', '\
+X',\n'3GP', 'X',\n'3HB', 'X',\n'3HC', 'X',\n'3HP',\
+ 'X',\n'3IB', 'X',\n'3ID', 'X',\n'3IN', 'X',\n'3MA\
+', 'X',\n'3MB', 'X',\n'3MC', 'X',\n'3MD', 'D',\n'3\
+MF', 'X',\n'3MP', 'X',\n'3MT', 'X',\n'3OL', 'X',\n\
+'3PA', 'X',\n'3PG', 'X',\n'3PO', 'X',\n'3PP', 'X',\
+\n'3PY', 'X',\n'49A', 'X',\n'4AB', 'X',\n'4AM', 'X\
+',\n'4AN', 'X',\n'4AP', 'X',\n'4BA', 'X',\n'4BT', \
+'X',\n'4CA', 'X',\n'4CO', 'X',\n'4HP', 'X',\n'4IP'\
+, 'X',\n'4MO', 'X',\n'4MV', 'X',\n'4MZ', 'X',\n'4N\
+C', 'X',\n'4NP', 'X',\n'4OX', 'X',\n'4PB', 'X',\n'\
+4PN', 'X',\n'4PP', 'X',\n'4SC', 'X',\n'4SU', 'X',\\
+n'4TB', 'X',\n'55C', 'X',\n'5AD', 'X',\n'5AN', 'X'\
+,\n'5AT', 'X',\n'5CM', 'X',\n'5GP', 'X',\n'5HP', '\
+E',\n'5HT', 'X',\n'5IT', 'X',\n'5IU', 'X',\n'5MB',\
+ 'X',\n'5MC', 'X',\n'5MD', 'X',\n'5MP', 'X',\n'5MU\
+', 'X',\n'5NC', 'X',\n'5OB', 'X',\n'5PA', 'X',\n'5\
+PV', 'X',\n'6AB', 'X',\n'6CT', 'X',\n'6HA', 'X',\n\
+'6HC', 'X',\n'6HG', 'X',\n'6HT', 'X',\n'6IN', 'X',\
+\n'6MO', 'X',\n'6MP', 'X',\n'6PG', 'X',\n'6WO', 'X\
+',\n'70U', 'X',\n'7DG', 'X',\n'7HP', 'X',\n'7I2', \
+'X',\n'7MG', 'X',\n'7MQ', 'X',\n'7NI', 'X',\n'87Y'\
+, 'X',\n'8AD', 'X',\n'8BR', 'X',\n'8IG', 'X',\n'8I\
+N', 'X',\n'8OG', 'X',\n'95A', 'X',\n'9AD', 'X',\n'\
+9AM', 'X',\n'9AP', 'X',\n'9DG', 'X',\n'9DI', 'X',\\
+n'9HX', 'X',\n'9OH', 'X',\n'9TA', 'X',\n'A12', 'X'\
+,\n'A15', 'X',\n'A23', 'X',\n'A24', 'X',\n'A26', '\
+X',\n'A2G', 'X',\n'A2P', 'X',\n'A32', 'X',\n'A3P',\
+ 'X',\n'A4P', 'X',\n'A5P', 'X',\n'A70', 'X',\n'A76\
+', 'X',\n'A77', 'X',\n'A78', 'X',\n'A79', 'X',\n'A\
+80', 'X',\n'A85', 'X',\n'A88', 'X',\n'A9A', 'X',\n\
+'AA3', 'X',\n'AA4', 'X',\n'AA6', 'X',\n'AAA', 'X',\
+\n'AAB', 'X',\n'AAC', 'X',\n'AAE', 'X',\n'AAG', 'R\
+',\n'AAH', 'X',\n'AAM', 'X',\n'AAN', 'X',\n'AAP', \
+'X',\n'AAR', 'R',\n'AAS', 'X',\n'AAT', 'X',\n'ABA'\
+, 'X',\n'ABC', 'X',\n'ABD', 'X',\n'ABE', 'X',\n'AB\
+H', 'X',\n'ABI', 'X',\n'ABK', 'X',\n'ABM', 'X',\n'\
+ABN', 'X',\n'ABP', 'X',\n'ABR', 'X',\n'ABS', 'X',\\
+n'ABU', 'X',\n'AC1', 'X',\n'AC2', 'X',\n'ACA', 'X'\
+,\n'ACB', 'D',\n'ACC', 'C',\n'ACD', 'X',\n'ACE', '\
+X',\n'ACH', 'X',\n'ACI', 'X',\n'ACL', 'R',\n'ACM',\
+ 'X',\n'ACN', 'X',\n'ACO', 'X',\n'ACP', 'X',\n'ACQ\
+', 'X',\n'ACR', 'X',\n'ACS', 'X',\n'ACT', 'X',\n'A\
+CV', 'V',\n'ACX', 'X',\n'ACY', 'X',\n'AD2', 'X',\n\
+'AD3', 'X',\n'ADC', 'X',\n'ADD', 'X',\n'ADE', 'X',\
+\n'ADH', 'X',\n'ADI', 'X',\n'ADM', 'X',\n'ADN', 'X\
+',\n'ADP', 'X',\n'ADQ', 'X',\n'ADR', 'X',\n'ADS', \
+'X',\n'ADT', 'X',\n'ADU', 'X',\n'ADW', 'X',\n'ADX'\
+, 'X',\n'AE2', 'X',\n'AEA', 'X',\n'AEB', 'X',\n'AE\
+I', 'D',\n'AEN', 'X',\n'AET', 'T',\n'AF1', 'X',\n'\
+AF3', 'X',\n'AFA', 'D',\n'AFP', 'X',\n'AG7', 'X',\\
+n'AGB', 'X',\n'AGF', 'X',\n'AGL', 'X',\n'AGM', 'R'\
+,\n'AGN', 'X',\n'AGP', 'X',\n'AGS', 'X',\n'AGU', '\
+X',\n'AH0', 'X',\n'AH1', 'X',\n'AHA', 'X',\n'AHB',\
+ 'D',\n'AHC', 'X',\n'AHF', 'X',\n'AHG', 'X',\n'AHH\
+', 'X',\n'AHM', 'X',\n'AHO', 'X',\n'AHP', 'X',\n'A\
+HS', 'X',\n'AHT', 'Y',\n'AHU', 'X',\n'AHX', 'X',\n\
+'AI1', 'X',\n'AI2', 'X',\n'AIB', 'X',\n'AIC', 'X',\
+\n'AIM', 'X',\n'AIP', 'X',\n'AIQ', 'X',\n'AIR', 'X\
+',\n'AJ3', 'X',\n'AKB', 'X',\n'AKG', 'X',\n'AKR', \
+'X',\n'AL1', 'X',\n'AL2', 'X',\n'AL3', 'X',\n'AL4'\
+, 'X',\n'AL5', 'X',\n'AL6', 'X',\n'AL7', 'X',\n'AL\
+8', 'X',\n'AL9', 'X',\n'ALA', 'A',\n'ALB', 'X',\n'\
+ALC', 'X',\n'ALD', 'L',\n'ALE', 'X',\n'ALF', 'X',\\
+n'ALG', 'X',\n'ALL', 'X',\n'ALM', 'A',\n'ALN', 'A'\
+,\n'ALO', 'T',\n'ALP', 'X',\n'ALQ', 'X',\n'ALR', '\
+X',\n'ALS', 'X',\n'ALT', 'A',\n'ALY', 'K',\n'ALZ',\
+ 'X',\n'AMA', 'X',\n'AMB', 'X',\n'AMC', 'X',\n'AMD\
+', 'X',\n'AMG', 'X',\n'AMH', 'X',\n'AMI', 'X',\n'A\
+ML', 'X',\n'AMN', 'X',\n'AMO', 'X',\n'AMP', 'X',\n\
+'AMQ', 'X',\n'AMR', 'X',\n'AMS', 'X',\n'AMT', 'X',\
+\n'AMU', 'X',\n'AMW', 'X',\n'AMX', 'X',\n'AMY', 'X\
+',\n'ANA', 'X',\n'ANB', 'X',\n'ANC', 'X',\n'AND', \
+'X',\n'ANE', 'X',\n'ANI', 'X',\n'ANL', 'X',\n'ANO'\
+, 'X',\n'ANP', 'X',\n'ANS', 'X',\n'ANT', 'X',\n'AO\
+E', 'X',\n'AOP', 'X',\n'AP1', 'X',\n'AP2', 'X',\n'\
+AP3', 'X',\n'AP4', 'X',\n'AP5', 'X',\n'AP6', 'X',\\
+n'APA', 'X',\n'APB', 'X',\n'APC', 'X',\n'APE', 'F'\
+,\n'APF', 'X',\n'APG', 'X',\n'APH', 'A',\n'API', '\
+X',\n'APL', 'X',\n'APM', 'X',\n'APN', 'G',\n'APP',\
+ 'X',\n'APQ', 'X',\n'APR', 'X',\n'APS', 'X',\n'APT\
+', 'X',\n'APU', 'X',\n'APX', 'X',\n'APY', 'X',\n'A\
+PZ', 'X',\n'AQS', 'X',\n'AR1', 'X',\n'AR2', 'X',\n\
+'ARA', 'X',\n'ARB', 'X',\n'ARC', 'X',\n'ARD', 'X',\
+\n'ARG', 'R',\n'ARH', 'X',\n'ARI', 'X',\n'ARM', 'R\
+',\n'ARN', 'X',\n'ARO', 'R',\n'ARP', 'X',\n'ARQ', \
+'X',\n'ARS', 'X',\n'AS1', 'R',\n'AS2', 'X',\n'ASA'\
+, 'D',\n'ASB', 'D',\n'ASC', 'X',\n'ASD', 'X',\n'AS\
+E', 'X',\n'ASF', 'X',\n'ASI', 'X',\n'ASK', 'D',\n'\
+ASL', 'X',\n'ASM', 'N',\n'ASO', 'X',\n'ASP', 'D',\\
+n'ASQ', 'X',\n'ASU', 'X',\n'ATA', 'X',\n'ATC', 'X'\
+,\n'ATD', 'X',\n'ATF', 'X',\n'ATG', 'X',\n'ATH', '\
+X',\n'ATM', 'X',\n'ATO', 'X',\n'ATP', 'X',\n'ATQ',\
+ 'X',\n'ATR', 'X',\n'ATT', 'X',\n'ATY', 'X',\n'ATZ\
+', 'X',\n'AUC', 'X',\n'AUR', 'X',\n'AVG', 'X',\n'A\
+XP', 'X',\n'AYA', 'A',\n'AZ2', 'X',\n'AZA', 'X',\n\
+'AZC', 'X',\n'AZD', 'X',\n'AZE', 'X',\n'AZI', 'X',\
+\n'AZL', 'X',\n'AZM', 'X',\n'AZR', 'X',\n'AZT', 'X\
+',\n'B12', 'X',\n'B1F', 'F',\n'B2A', 'A',\n'B2F', \
+'F',\n'B2I', 'I',\n'B2V', 'V',\n'B3I', 'X',\n'B3P'\
+, 'X',\n'B7G', 'X',\n'B96', 'X',\n'B9A', 'X',\n'BA\
+1', 'X',\n'BAA', 'X',\n'BAB', 'X',\n'BAC', 'X',\n'\
+BAF', 'X',\n'BAH', 'X',\n'BAI', 'X',\n'BAK', 'X',\\
+n'BAL', 'A',\n'BAM', 'X',\n'BAO', 'X',\n'BAP', 'X'\
+,\n'BAR', 'X',\n'BAS', 'X',\n'BAT', 'F',\n'BAY', '\
+X',\n'BAZ', 'X',\n'BB1', 'X',\n'BB2', 'X',\n'BBA',\
+ 'X',\n'BBH', 'X',\n'BBS', 'X',\n'BBT', 'X',\n'BBZ\
+', 'X',\n'BCA', 'X',\n'BCB', 'X',\n'BCC', 'X',\n'B\
+CD', 'X',\n'BCL', 'X',\n'BCN', 'X',\n'BCR', 'X',\n\
+'BCS', 'C',\n'BCT', 'X',\n'BCY', 'X',\n'BCZ', 'X',\
+\n'BDA', 'X',\n'BDG', 'X',\n'BDK', 'X',\n'BDM', 'X\
+',\n'BDN', 'X',\n'BDS', 'X',\n'BE1', 'X',\n'BE2', \
+'X',\n'BEA', 'X',\n'BEF', 'X',\n'BEN', 'X',\n'BEO'\
+, 'X',\n'BEP', 'X',\n'BER', 'X',\n'BES', 'X',\n'BE\
+T', 'X',\n'BEZ', 'X',\n'BF2', 'X',\n'BFA', 'X',\n'\
+BFD', 'X',\n'BFP', 'X',\n'BFS', 'X',\n'BFU', 'X',\\
+n'BG6', 'X',\n'BGF', 'X',\n'BGG', 'X',\n'BGL', 'X'\
+,\n'BGN', 'X',\n'BGP', 'X',\n'BGX', 'X',\n'BH4', '\
+X',\n'BHA', 'X',\n'BHC', 'X',\n'BHD', 'D',\n'BHO',\
+ 'X',\n'BHS', 'X',\n'BIC', 'X',\n'BIN', 'X',\n'BIO\
+', 'X',\n'BIP', 'X',\n'BIS', 'X',\n'BIZ', 'X',\n'B\
+JH', 'X',\n'BJI', 'X',\n'BJP', 'X',\n'BLA', 'X',\n\
+'BLB', 'X',\n'BLE', 'L',\n'BLG', 'P',\n'BLI', 'X',\
+\n'BLM', 'X',\n'BLV', 'X',\n'BLY', 'K',\n'BM1', 'X\
+',\n'BM2', 'X',\n'BM5', 'X',\n'BM9', 'X',\n'BMA', \
+'X',\n'BMD', 'X',\n'BME', 'X',\n'BMP', 'X',\n'BMQ'\
+, 'X',\n'BMS', 'X',\n'BMT', 'T',\n'BMU', 'X',\n'BM\
+Y', 'X',\n'BMZ', 'X',\n'BNA', 'X',\n'BNG', 'X',\n'\
+BNI', 'X',\n'BNN', 'F',\n'BNO', 'L',\n'BNS', 'X',\\
+n'BNZ', 'X',\n'BO3', 'X',\n'BO4', 'X',\n'BOC', 'X'\
+,\n'BOG', 'X',\n'BOM', 'X',\n'BOT', 'X',\n'BOX', '\
+X',\n'BOZ', 'X',\n'BPA', 'X',\n'BPB', 'X',\n'BPD',\
+ 'X',\n'BPG', 'X',\n'BPH', 'X',\n'BPI', 'X',\n'BPJ\
+', 'X',\n'BPM', 'X',\n'BPN', 'X',\n'BPO', 'X',\n'B\
+PP', 'X',\n'BPT', 'X',\n'BPY', 'X',\n'BRB', 'X',\n\
+'BRC', 'X',\n'BRE', 'X',\n'BRI', 'X',\n'BRL', 'X',\
+\n'BRM', 'X',\n'BRN', 'X',\n'BRO', 'X',\n'BRS', 'X\
+',\n'BRU', 'X',\n'BRZ', 'X',\n'BSB', 'X',\n'BSI', \
+'X',\n'BSP', 'X',\n'BT1', 'X',\n'BT2', 'X',\n'BT3'\
+, 'X',\n'BTA', 'L',\n'BTB', 'X',\n'BTC', 'C',\n'BT\
+D', 'X',\n'BTN', 'X',\n'BTP', 'X',\n'BTR', 'W',\n'\
+BU1', 'X',\n'BUA', 'X',\n'BUB', 'X',\n'BUC', 'X',\\
+n'BUG', 'X',\n'BUL', 'X',\n'BUM', 'X',\n'BUQ', 'X'\
+,\n'BUT', 'X',\n'BVD', 'X',\n'BX3', 'X',\n'BYS', '\
+X',\n'BZ1', 'X',\n'BZA', 'X',\n'BZB', 'X',\n'BZC',\
+ 'X',\n'BZD', 'X',\n'BZF', 'X',\n'BZI', 'X',\n'BZM\
+', 'X',\n'BZO', 'X',\n'BZP', 'X',\n'BZQ', 'X',\n'B\
+ZS', 'X',\n'BZT', 'X',\n'C02', 'X',\n'C11', 'X',\n\
+'C1O', 'X',\n'C20', 'X',\n'C24', 'X',\n'C2F', 'X',\
+\n'C2O', 'X',\n'C2P', 'X',\n'C3M', 'X',\n'C3P', 'X\
+',\n'C3X', 'X',\n'C48', 'X',\n'C4M', 'X',\n'C4X', \
+'X',\n'C5C', 'X',\n'C5M', 'X',\n'C5P', 'X',\n'C5X'\
+, 'X',\n'C60', 'X',\n'C6C', 'X',\n'C6M', 'X',\n'C7\
+8', 'X',\n'C8E', 'X',\n'CA3', 'X',\n'CA5', 'X',\n'\
+CAA', 'X',\n'CAB', 'X',\n'CAC', 'X',\n'CAD', 'X',\\
+n'CAF', 'C',\n'CAG', 'X',\n'CAH', 'X',\n'CAL', 'X'\
+,\n'CAM', 'X',\n'CAN', 'X',\n'CAO', 'X',\n'CAP', '\
+X',\n'CAQ', 'X',\n'CAR', 'X',\n'CAS', 'C',\n'CAT',\
+ 'X',\n'CAV', 'X',\n'CAY', 'C',\n'CAZ', 'X',\n'CB3\
+', 'X',\n'CB4', 'X',\n'CBA', 'X',\n'CBD', 'X',\n'C\
+BG', 'X',\n'CBI', 'X',\n'CBL', 'X',\n'CBM', 'X',\n\
+'CBN', 'X',\n'CBO', 'X',\n'CBP', 'X',\n'CBS', 'X',\
+\n'CBX', 'X',\n'CBZ', 'X',\n'CC0', 'X',\n'CC1', 'X\
+',\n'CCC', 'X',\n'CCH', 'X',\n'CCI', 'X',\n'CCM', \
+'X',\n'CCN', 'X',\n'CCO', 'X',\n'CCP', 'X',\n'CCR'\
+, 'X',\n'CCS', 'C',\n'CCV', 'X',\n'CCY', 'X',\n'CD\
+1', 'X',\n'CDC', 'X',\n'CDE', 'X',\n'CDF', 'X',\n'\
+CDI', 'X',\n'CDL', 'X',\n'CDM', 'X',\n'CDP', 'X',\\
+n'CDR', 'X',\n'CDU', 'X',\n'CE1', 'X',\n'CEA', 'C'\
+,\n'CEB', 'X',\n'CEC', 'X',\n'CED', 'X',\n'CEF', '\
+X',\n'CEH', 'X',\n'CEM', 'X',\n'CEO', 'X',\n'CEP',\
+ 'X',\n'CEQ', 'X',\n'CER', 'X',\n'CES', 'G',\n'CET\
+', 'X',\n'CFC', 'X',\n'CFF', 'X',\n'CFM', 'X',\n'C\
+FO', 'X',\n'CFP', 'X',\n'CFS', 'X',\n'CFX', 'X',\n\
+'CGN', 'X',\n'CGP', 'X',\n'CGS', 'X',\n'CGU', 'E',\
+\n'CH2', 'X',\n'CH3', 'X',\n'CHA', 'X',\n'CHB', 'X\
+',\n'CHD', 'X',\n'CHF', 'X',\n'CHG', 'G',\n'CHI', \
+'X',\n'CHN', 'X',\n'CHO', 'X',\n'CHP', 'G',\n'CHR'\
+, 'X',\n'CHS', 'F',\n'CHT', 'X',\n'CHX', 'X',\n'CI\
+C', 'X',\n'CIN', 'X',\n'CIP', 'X',\n'CIR', 'X',\n'\
+CIT', 'X',\n'CIU', 'X',\n'CKI', 'X',\n'CL1', 'X',\\
+n'CL2', 'X',\n'CLA', 'X',\n'CLB', 'A',\n'CLC', 'S'\
+,\n'CLD', 'A',\n'CLE', 'L',\n'CLF', 'X',\n'CLK', '\
+S',\n'CLL', 'X',\n'CLM', 'X',\n'CLN', 'X',\n'CLO',\
+ 'X',\n'CLP', 'X',\n'CLQ', 'X',\n'CLR', 'X',\n'CLS\
+', 'X',\n'CLT', 'X',\n'CLX', 'X',\n'CLY', 'X',\n'C\
+MA', 'R',\n'CMC', 'X',\n'CMD', 'X',\n'CME', 'C',\n\
+'CMG', 'X',\n'CMK', 'X',\n'CMN', 'X',\n'CMO', 'X',\
+\n'CMP', 'X',\n'CMR', 'X',\n'CMS', 'X',\n'CMT', 'C\
+',\n'CMX', 'X',\n'CNA', 'X',\n'CNC', 'X',\n'CND', \
+'X',\n'CNH', 'X',\n'CNM', 'X',\n'CNN', 'X',\n'CNO'\
+, 'X',\n'CNP', 'X',\n'CO2', 'X',\n'CO3', 'X',\n'CO\
+5', 'X',\n'CO8', 'X',\n'COA', 'X',\n'COB', 'X',\n'\
+COC', 'X',\n'COD', 'X',\n'COE', 'X',\n'COF', 'X',\\
+n'COH', 'X',\n'COI', 'X',\n'COJ', 'X',\n'COL', 'X'\
+,\n'COM', 'X',\n'CON', 'X',\n'COP', 'X',\n'COR', '\
+X',\n'COS', 'X',\n'COT', 'X',\n'COY', 'X',\n'CP1',\
+ 'G',\n'CP2', 'X',\n'CP4', 'X',\n'CPA', 'X',\n'CPB\
+', 'X',\n'CPC', 'X',\n'CPD', 'X',\n'CPG', 'X',\n'C\
+PH', 'X',\n'CPI', 'X',\n'CPM', 'X',\n'CPN', 'G',\n\
+'CPO', 'X',\n'CPP', 'X',\n'CPQ', 'X',\n'CPR', 'X',\
+\n'CPS', 'X',\n'CPT', 'X',\n'CPU', 'X',\n'CPV', 'X\
+',\n'CPY', 'X',\n'CR1', 'X',\n'CR6', 'X',\n'CRA', \
+'X',\n'CRB', 'X',\n'CRC', 'X',\n'CRG', 'X',\n'CRH'\
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+N',\n'PP9', 'X',\n'PPB', 'X',\n'PPC', 'X',\n'PPD',\
+ 'X',\n'PPE', 'E',\n'PPG', 'X',\n'PPH', 'F',\n'PPI\
+', 'X',\n'PPJ', 'V',\n'PPL', 'X',\n'PPM', 'X',\n'P\
+PN', 'A',\n'PPO', 'X',\n'PPP', 'X',\n'PPQ', 'X',\n\
+'PPR', 'X',\n'PPS', 'X',\n'PPT', 'X',\n'PPU', 'X',\
+\n'PPX', 'F',\n'PPY', 'X',\n'PPZ', 'X',\n'PQ0', 'X\
+',\n'PQN', 'X',\n'PQQ', 'X',\n'PR1', 'X',\n'PR2', \
+'X',\n'PR3', 'X',\n'PRA', 'X',\n'PRB', 'X',\n'PRC'\
+, 'X',\n'PRD', 'X',\n'PRE', 'X',\n'PRF', 'X',\n'PR\
+H', 'X',\n'PRI', 'P',\n'PRL', 'X',\n'PRN', 'X',\n'\
+PRO', 'P',\n'PRP', 'X',\n'PRR', 'A',\n'PRS', 'P',\\
+n'PRZ', 'X',\n'PS0', 'X',\n'PSA', 'X',\n'PSD', 'X'\
+,\n'PSE', 'X',\n'PSF', 'S',\n'PSG', 'X',\n'PSI', '\
+X',\n'PSO', 'X',\n'PSQ', 'X',\n'PSS', 'X',\n'PST',\
+ 'X',\n'PSU', 'X',\n'PT1', 'X',\n'PT3', 'X',\n'PTA\
+', 'X',\n'PTC', 'X',\n'PTD', 'X',\n'PTE', 'X',\n'P\
+TH', 'Y',\n'PTL', 'X',\n'PTM', 'Y',\n'PTN', 'X',\n\
+'PTO', 'X',\n'PTP', 'X',\n'PTR', 'Y',\n'PTS', 'X',\
+\n'PTT', 'X',\n'PTU', 'X',\n'PTY', 'X',\n'PUA', 'X\
+',\n'PUB', 'X',\n'PUR', 'X',\n'PUT', 'X',\n'PVA', \
+'X',\n'PVB', 'X',\n'PVH', 'H',\n'PVL', 'X',\n'PXA'\
+, 'X',\n'PXF', 'X',\n'PXG', 'X',\n'PXP', 'X',\n'PX\
+Y', 'X',\n'PXZ', 'X',\n'PY2', 'X',\n'PY4', 'X',\n'\
+PY5', 'X',\n'PY6', 'X',\n'PYA', 'A',\n'PYC', 'X',\\
+n'PYD', 'X',\n'PYE', 'X',\n'PYL', 'X',\n'PYM', 'X'\
+,\n'PYO', 'X',\n'PYP', 'X',\n'PYQ', 'X',\n'PYR', '\
+X',\n'PYS', 'X',\n'PYT', 'X',\n'PYX', 'X',\n'PYY',\
+ 'X',\n'PYZ', 'X',\n'PZQ', 'X',\n'Q82', 'X',\n'QNC\
+', 'X',\n'QND', 'X',\n'QSI', 'Q',\n'QTR', 'X',\n'Q\
+UA', 'X',\n'QUE', 'X',\n'QUI', 'X',\n'QUO', 'X',\n\
+'R11', 'X',\n'R12', 'X',\n'R13', 'X',\n'R18', 'X',\
+\n'R1P', 'X',\n'R56', 'X',\n'R5P', 'X',\n'RA2', 'X\
+',\n'RAD', 'X',\n'RAI', 'X',\n'RAL', 'X',\n'RAM', \
+'X',\n'RAN', 'X',\n'RAP', 'X',\n'RBF', 'X',\n'RBU'\
+, 'X',\n'RCA', 'X',\n'RCL', 'X',\n'RCO', 'X',\n'RD\
+C', 'X',\n'RDF', 'W',\n'RE9', 'X',\n'REA', 'X',\n'\
+RED', 'K',\n'REO', 'X',\n'REP', 'X',\n'RET', 'X',\\
+n'RFA', 'X',\n'RFB', 'X',\n'RFL', 'X',\n'RFP', 'X'\
+,\n'RG1', 'X',\n'RGS', 'X',\n'RH1', 'X',\n'RHA', '\
+X',\n'RHC', 'X',\n'RHD', 'X',\n'RHM', 'X',\n'RHO',\
+ 'X',\n'RHQ', 'X',\n'RHS', 'X',\n'RIA', 'X',\n'RIB\
+', 'X',\n'RIC', 'X',\n'RIF', 'X',\n'RIN', 'X',\n'R\
+IP', 'X',\n'RIT', 'X',\n'RMB', 'X',\n'RMN', 'X',\n\
+'RMP', 'X',\n'RNG', 'X',\n'RNS', 'X',\n'RNT', 'X',\
+\n'RO2', 'X',\n'RO4', 'X',\n'ROC', 'N',\n'ROI', 'X\
+',\n'ROM', 'X',\n'RON', 'V',\n'ROP', 'X',\n'ROS', \
+'X',\n'ROX', 'X',\n'RPA', 'X',\n'RPD', 'X',\n'RPH'\
+, 'X',\n'RPL', 'X',\n'RPP', 'X',\n'RPR', 'X',\n'RP\
+X', 'X',\n'RQ3', 'X',\n'RR1', 'X',\n'RR6', 'X',\n'\
+RRS', 'X',\n'RS1', 'X',\n'RS2', 'X',\n'RS7', 'X',\\
+n'RSS', 'X',\n'RTA', 'X',\n'RTB', 'X',\n'RTC', 'X'\
+,\n'RTL', 'X',\n'RUB', 'X',\n'RUN', 'X',\n'RWJ', '\
+X',\n'RXP', 'X',\n'S02', 'X',\n'S11', 'X',\n'S1H',\
+ 'S',\n'S27', 'X',\n'S2C', 'C',\n'S3P', 'X',\n'S4U\
+', 'X',\n'S57', 'X',\n'S58', 'X',\n'S5H', 'X',\n'S\
+6G', 'X',\n'S80', 'X',\n'SAA', 'X',\n'SAB', 'X',\n\
+'SAC', 'S',\n'SAD', 'X',\n'SAE', 'X',\n'SAF', 'X',\
+\n'SAH', 'C',\n'SAI', 'C',\n'SAL', 'X',\n'SAM', 'M\
+',\n'SAN', 'X',\n'SAP', 'X',\n'SAR', 'X',\n'SAS', \
+'X',\n'SB1', 'X',\n'SB2', 'X',\n'SB3', 'X',\n'SB4'\
+, 'X',\n'SB5', 'X',\n'SB6', 'X',\n'SBA', 'L',\n'SB\
+B', 'X',\n'SBD', 'A',\n'SBI', 'X',\n'SBL', 'A',\n'\
+SBN', 'X',\n'SBO', 'X',\n'SBR', 'X',\n'SBS', 'X',\\
+n'SBT', 'X',\n'SBU', 'X',\n'SBX', 'X',\n'SC4', 'X'\
+,\n'SCA', 'X',\n'SCC', 'X',\n'SCD', 'X',\n'SCH', '\
+C',\n'SCI', 'X',\n'SCL', 'X',\n'SCM', 'X',\n'SCN',\
+ 'X',\n'SCO', 'X',\n'SCP', 'S',\n'SCR', 'X',\n'SCS\
+', 'X',\n'SCV', 'C',\n'SCY', 'C',\n'SD8', 'X',\n'S\
+DK', 'X',\n'SDZ', 'X',\n'SE4', 'X',\n'SEA', 'X',\n\
+'SEB', 'S',\n'SEC', 'X',\n'SEG', 'A',\n'SEI', 'X',\
+\n'SEL', 'S',\n'SEM', 'X',\n'SEO', 'X',\n'SEP', 'S\
+',\n'SER', 'S',\n'SES', 'X',\n'SET', 'S',\n'SEU', \
+'X',\n'SF4', 'X',\n'SFG', 'X',\n'SFN', 'X',\n'SFO'\
+, 'X',\n'SGA', 'X',\n'SGC', 'X',\n'SGL', 'X',\n'SG\
+M', 'X',\n'SGN', 'X',\n'SGP', 'X',\n'SHA', 'X',\n'\
+SHC', 'X',\n'SHF', 'X',\n'SHH', 'X',\n'SHP', 'G',\\
+n'SHR', 'E',\n'SHT', 'T',\n'SHU', 'X',\n'SI2', 'X'\
+,\n'SIA', 'X',\n'SIF', 'X',\n'SIG', 'X',\n'SIH', '\
+X',\n'SIM', 'X',\n'SIN', 'X',\n'SKD', 'X',\n'SKF',\
+ 'X',\n'SLB', 'X',\n'SLE', 'X',\n'SLZ', 'K',\n'SMA\
+', 'X',\n'SMC', 'C',\n'SME', 'M',\n'SML', 'X',\n'S\
+MM', 'M',\n'SMN', 'X',\n'SMP', 'X',\n'SMS', 'X',\n\
+'SN1', 'X',\n'SN6', 'X',\n'SN7', 'X',\n'SNC', 'C',\
+\n'SNN', 'X',\n'SNP', 'X',\n'SO1', 'X',\n'SO2', 'X\
+',\n'SO3', 'X',\n'SO4', 'X',\n'SOA', 'X',\n'SOC', \
+'C',\n'SOM', 'X',\n'SOR', 'X',\n'SOT', 'X',\n'SOX'\
+, 'X',\n'SPA', 'X',\n'SPB', 'X',\n'SPC', 'X',\n'SP\
+D', 'X',\n'SPE', 'X',\n'SPG', 'X',\n'SPH', 'X',\n'\
+SPI', 'X',\n'SPK', 'X',\n'SPM', 'X',\n'SPN', 'X',\\
+n'SPO', 'X',\n'SPP', 'X',\n'SPS', 'X',\n'SPY', 'X'\
+,\n'SQU', 'X',\n'SRA', 'X',\n'SRB', 'X',\n'SRD', '\
+X',\n'SRL', 'X',\n'SRM', 'X',\n'SRS', 'X',\n'SRY',\
+ 'X',\n'SSA', 'X',\n'SSB', 'X',\n'SSG', 'X',\n'SSP\
+', 'X',\n'ST1', 'X',\n'ST2', 'X',\n'ST3', 'X',\n'S\
+T4', 'X',\n'ST5', 'X',\n'ST6', 'X',\n'STA', 'X',\n\
+'STB', 'X',\n'STE', 'X',\n'STG', 'X',\n'STI', 'X',\
+\n'STL', 'X',\n'STN', 'X',\n'STO', 'X',\n'STP', 'X\
+',\n'STR', 'X',\n'STU', 'X',\n'STY', 'Y',\n'SU1', \
+'X',\n'SU2', 'X',\n'SUC', 'X',\n'SUI', 'X',\n'SUL'\
+, 'X',\n'SUR', 'X',\n'SVA', 'S',\n'SWA', 'X',\n'T1\
+6', 'X',\n'T19', 'X',\n'T23', 'X',\n'T29', 'X',\n'\
+T33', 'X',\n'T3P', 'X',\n'T42', 'A',\n'T44', 'X',\\
+n'T5A', 'X',\n'T6A', 'T',\n'T6P', 'X',\n'T80', 'X'\
+,\n'T87', 'X',\n'TA1', 'X',\n'TAA', 'X',\n'TAB', '\
+X',\n'TAC', 'X',\n'TAD', 'X',\n'TAF', 'X',\n'TAM',\
+ 'X',\n'TAP', 'X',\n'TAR', 'X',\n'TAS', 'X',\n'TAU\
+', 'X',\n'TAX', 'X',\n'TAZ', 'X',\n'TB9', 'X',\n'T\
+BA', 'X',\n'TBD', 'X',\n'TBG', 'G',\n'TBH', 'X',\n\
+'TBM', 'T',\n'TBO', 'X',\n'TBP', 'X',\n'TBR', 'X',\
+\n'TBS', 'X',\n'TBT', 'X',\n'TBU', 'X',\n'TBZ', 'X\
+',\n'TC4', 'X',\n'TCA', 'X',\n'TCB', 'X',\n'TCH', \
+'X',\n'TCK', 'X',\n'TCL', 'X',\n'TCM', 'X',\n'TCN'\
+, 'X',\n'TCP', 'X',\n'TCR', 'W',\n'TCS', 'X',\n'TC\
+Z', 'X',\n'TDA', 'X',\n'TDB', 'X',\n'TDG', 'X',\n'\
+TDP', 'X',\n'TDR', 'X',\n'TDX', 'X',\n'TEA', 'X',\\
+n'TEM', 'X',\n'TEN', 'X',\n'TEO', 'X',\n'TEP', 'X'\
+,\n'TER', 'X',\n'TES', 'X',\n'TET', 'X',\n'TFA', '\
+X',\n'TFB', 'X',\n'TFH', 'X',\n'TFI', 'X',\n'TFK',\
+ 'X',\n'TFP', 'X',\n'THA', 'X',\n'THB', 'X',\n'THC\
+', 'T',\n'THD', 'X',\n'THE', 'X',\n'THF', 'X',\n'T\
+HJ', 'X',\n'THK', 'X',\n'THM', 'X',\n'THN', 'X',\n\
+'THO', 'T',\n'THP', 'X',\n'THQ', 'X',\n'THR', 'T',\
+\n'THS', 'X',\n'THT', 'X',\n'THU', 'X',\n'THX', 'X\
+',\n'THZ', 'X',\n'TI1', 'X',\n'TI2', 'X',\n'TI3', \
+'P',\n'TIA', 'X',\n'TIH', 'A',\n'TK4', 'X',\n'TLA'\
+, 'X',\n'TLC', 'X',\n'TLM', 'X',\n'TLN', 'X',\n'TL\
+X', 'X',\n'TM5', 'X',\n'TM6', 'X',\n'TMA', 'X',\n'\
+TMB', 'T',\n'TMC', 'X',\n'TMD', 'T',\n'TME', 'X',\\
+n'TMF', 'X',\n'TML', 'K',\n'TMM', 'X',\n'TMN', 'X'\
+,\n'TMP', 'X',\n'TMQ', 'X',\n'TMR', 'X',\n'TMT', '\
+X',\n'TMZ', 'X',\n'TNB', 'C',\n'TND', 'X',\n'TNK',\
+ 'X',\n'TNP', 'X',\n'TNT', 'X',\n'TOA', 'X',\n'TOB\
+', 'X',\n'TOC', 'X',\n'TOL', 'X',\n'TOP', 'X',\n'T\
+OS', 'X',\n'TOT', 'X',\n'TP1', 'G',\n'TP2', 'P',\n\
+'TP3', 'E',\n'TP4', 'E',\n'TP7', 'T',\n'TPA', 'X',\
+\n'TPE', 'X',\n'TPF', 'X',\n'TPI', 'X',\n'TPL', 'W\
+',\n'TPM', 'X',\n'TPN', 'G',\n'TPO', 'T',\n'TPP', \
+'X',\n'TPQ', 'A',\n'TPR', 'P',\n'TPS', 'X',\n'TPT'\
+, 'X',\n'TPV', 'X',\n'TPX', 'X',\n'TPY', 'X',\n'TQ\
+3', 'X',\n'TQ4', 'X',\n'TQ5', 'X',\n'TQ6', 'X',\n'\
+TR1', 'X',\n'TRA', 'X',\n'TRB', 'X',\n'TRC', 'X',\\
+n'TRD', 'X',\n'TRE', 'X',\n'TRF', 'W',\n'TRG', 'K'\
+,\n'TRH', 'X',\n'TRI', 'X',\n'TRJ', 'X',\n'TRM', '\
+X',\n'TRN', 'W',\n'TRO', 'W',\n'TRP', 'W',\n'TRQ',\
+ 'X',\n'TRS', 'X',\n'TRX', 'W',\n'TRZ', 'X',\n'TS2\
+', 'X',\n'TS3', 'X',\n'TS4', 'X',\n'TS5', 'X',\n'T\
+SA', 'X',\n'TSB', 'X',\n'TSI', 'X',\n'TSM', 'X',\n\
+'TSN', 'X',\n'TSP', 'X',\n'TSU', 'X',\n'TTA', 'X',\
+\n'TTE', 'X',\n'TTN', 'X',\n'TTO', 'X',\n'TTP', 'X\
+',\n'TTX', 'X',\n'TXL', 'X',\n'TYA', 'Y',\n'TYB', \
+'Y',\n'TYD', 'X',\n'TYI', 'Y',\n'TYL', 'X',\n'TYM'\
+, 'W',\n'TYN', 'Y',\n'TYQ', 'Y',\n'TYR', 'Y',\n'TY\
+S', 'Y',\n'TYV', 'X',\n'TYY', 'A',\n'TZB', 'X',\n'\
+TZC', 'X',\n'TZE', 'X',\n'TZL', 'X',\n'TZO', 'X',\\
+n'TZP', 'X',\n'U01', 'X',\n'U02', 'X',\n'U03', 'X'\
+,\n'U04', 'X',\n'U05', 'X',\n'U0E', 'X',\n'U10', '\
+X',\n'U18', 'X',\n'U2G', 'X',\n'U3P', 'X',\n'U49',\
+ 'X',\n'U55', 'X',\n'U5P', 'X',\n'U66', 'X',\n'U89\
+', 'X',\n'U8U', 'X',\n'UAA', 'X',\n'UAG', 'A',\n'U\
+AP', 'X',\n'UAR', 'X',\n'UC1', 'X',\n'UC2', 'X',\n\
+'UC3', 'X',\n'UC4', 'X',\n'UD1', 'X',\n'UD2', 'X',\
+\n'UDP', 'X',\n'UDX', 'X',\n'UFG', 'X',\n'UFM', 'X\
+',\n'UFP', 'X',\n'UGA', 'X',\n'UIN', 'X',\n'UKP', \
+'A',\n'UM3', 'X',\n'UMA', 'A',\n'UMG', 'X',\n'UMP'\
+, 'X',\n'UNA', 'X',\n'UND', 'X',\n'UNI', 'X',\n'UN\
+K', 'X',\n'UNN', 'X',\n'UNX', 'X',\n'UP5', 'X',\n'\
+UP6', 'X',\n'UPA', 'X',\n'UPF', 'X',\n'UPG', 'X',\\
+n'UPP', 'X',\n'UQ1', 'X',\n'UQ2', 'X',\n'UQ6', 'X'\
+,\n'UR2', 'X',\n'URA', 'X',\n'URE', 'X',\n'URF', '\
+X',\n'URI', 'X',\n'URS', 'X',\n'UTP', 'X',\n'UVC',\
+ 'X',\n'UVW', 'X',\n'V35', 'X',\n'V36', 'X',\n'V4O\
+', 'X',\n'V7O', 'X',\n'VAA', 'V',\n'VAC', 'X',\n'V\
+AD', 'V',\n'VAF', 'V',\n'VAG', 'X',\n'VAL', 'V',\n\
+'VAN', 'X',\n'VAS', 'X',\n'VAX', 'X',\n'VDX', 'X',\
+\n'VDY', 'X',\n'VG1', 'X',\n'VIB', 'X',\n'VIR', 'X\
+',\n'VIT', 'X',\n'VK3', 'X',\n'VO3', 'X',\n'VO4', \
+'X',\n'VS1', 'F',\n'VS2', 'F',\n'VS3', 'F',\n'VS4'\
+, 'F',\n'VXA', 'X',\n'W01', 'X',\n'W02', 'X',\n'W0\
+3', 'X',\n'W11', 'X',\n'W33', 'X',\n'W35', 'X',\n'\
+W42', 'X',\n'W43', 'X',\n'W54', 'X',\n'W56', 'X',\\
+n'W59', 'X',\n'W71', 'X',\n'W84', 'X',\n'W8R', 'X'\
+,\n'W91', 'X',\n'WAY', 'X',\n'WCC', 'X',\n'WO2', '\
+X',\n'WO4', 'X',\n'WRB', 'X',\n'WRR', 'X',\n'WRS',\
+ 'X',\n'WW7', 'X',\n'X2F', 'X',\n'X7O', 'X',\n'XAA\
+', 'X',\n'XAN', 'X',\n'XAO', 'X',\n'XBB', 'X',\n'X\
+BP', 'X',\n'XDN', 'X',\n'XDP', 'X',\n'XIF', 'X',\n\
+'XIM', 'X',\n'XK2', 'X',\n'XL1', 'X',\n'XLS', 'X',\
+\n'XMP', 'X',\n'XN1', 'X',\n'XN2', 'X',\n'XN3', 'X\
+',\n'XUL', 'X',\n'XV6', 'X',\n'XYD', 'X',\n'XYH', \
+'X',\n'XYL', 'X',\n'XYP', 'X',\n'XYS', 'X',\n'YOF'\
+, 'Y',\n'YRR', 'X',\n'YT3', 'X',\n'YZ9', 'X',\n'Z3\
+4', 'G',\n'Z5A', 'X',\n'ZAF', 'X',\n'ZAP', 'X',\n'\
+ZEB', 'X',\n'ZEN', 'X',\n'ZES', 'X',\n'ZID', 'X',\\
+n'ZMR', 'X',\n'ZN3', 'X',\n'ZNH', 'X',\n'ZNO', 'X'\
+,\n'ZO3', 'X',\n'ZPR', 'P',\n'ZRA', 'A',\n'ZST', '\
+X',\n'ZYA', 'A',\n\n\n'ASN','N');\n} \n\n\nsub fil\
+e2head\n {\n my $file = shift;\n my $size = s\
+hift;\n my $f= new FileHandle;\n my $line;\n open \
+($f,$file);\n read ($f,$line, $size);\n close ($f)\
+;\n return $line;\n }\nsub file2tail\n {\
+\n my $file = shift;\n my $size = shift;\n my $f= \
+new FileHandle;\n my $line;\n \n open ($f,$file);\\
+n seek ($f,$size*-1, 2);\n read ($f,$line, $size);\
+\n close ($f);\n return $line;\n }\n\n\nsub v\
+tmpnam\n {\n my $r=rand(100000);\n my $f=\"fi\
+le.$r.$$\";\n while (-e $f)\n {\n $f=vtmpnam\
+();\n }\n push (@TMPFILE_LIST, $f);\n return $f;\
+\n }\n\nsub myexit\n {\n my $code=@_[0];\\
+n if ($CLEAN_EXIT_STARTED==1){return;}\n els\
+e {$CLEAN_EXIT_STARTED=1;}\n ### ONLY BARE EXIT\
+\n exit ($code);\n }\nsub set_error_lock\n \
+{\n my $name = shift;\n my $pid=$$;\n\n \
+ \n &lock4tc ($$,\"LERROR\", \"LSET\", \"\
+$$ -- ERROR: $name $PROGRAM\\n\");\n return;\\
+n }\nsub set_lock\n {\n my $pid=shift;\n \
+ my $msg= shift;\n my $p=getppid();\n &lock4\
+tc ($pid,\"LLOCK\",\"LRESET\",\"$p$msg\\n\");\n }\
+\nsub unset_lock\n {\n \n my $pid=shift;\\
+n &lock4tc ($pid,\"LLOCK\",\"LRELEASE\",\"\");\\
+n }\nsub shift_lock\n {\n my $from=shift;\n \
+ my $to=shift;\n my $from_type=shift;\n my \
+$to_type=shift;\n my $action=shift;\n my $ms\
+g;\n \n if (!&lock4tc($from, $from_type, \"L\
+CHECK\", \"\")){return 0;}\n $msg=&lock4tc ($fr\
+om, $from_type, \"LREAD\", \"\");\n &lock4tc ($\
+from, $from_type,\"LRELEASE\", $msg);\n &lock4t\
+c ($to, $to_type, $action, $msg);\n return;\n \
+}\nsub isshellpid\n {\n my $p=shift;\n if (\
+!lock4tc ($p, \"LLOCK\", \"LCHECK\")){return 0;}\n\
+ else\n {\n my $c=lock4tc($p, \"LLOCK\", \\
+"LREAD\");\n if ( $c=~/-SHELL-/){return 1;}\n \
+ }\n return 0;\n }\nsub isrootpid\n {\n if\
+(lock4tc (getppid(), \"LLOCK\", \"LCHECK\")){retur\
+n 0;}\n else {return 1;}\n }\nsub lock4tc\n {\\
+n my ($pid,$type,$action,$value)=@_;\n my $fna\
+me;\n my $host=hostname;\n \n if ($type eq \\
+"LLOCK\"){$fname=\"$LOCKDIR/.$pid.$host.lock4tcoff\
+ee\";}\n elsif ( $type eq \"LERROR\"){ $fname=\"\
+$LOCKDIR/.$pid.$host.error4tcoffee\";}\n elsif (\
+ $type eq \"LWARNING\"){ $fname=\"$LOCKDIR/.$pid.$\
+host.warning4tcoffee\";}\n \n if ($debug_lock)\
+\n {\n print STDERR \"\\n\\t---lock4tc(t\
+cg): $action => $fname =>$value (RD: $LOCKDIR)\\n\\
+";\n }\n\n if ($action eq \"LCHECK\") {re\
+turn -e $fname;}\n elsif ($action eq \"LREAD\"){\
+return file2string($fname);}\n elsif ($action eq\
+ \"LSET\") {return string2file ($value, $fname, \"\
+>>\");}\n elsif ($action eq \"LRESET\") {return \
+string2file ($value, $fname, \">\");}\n elsif ($\
+action eq \"LRELEASE\") \n {\n if ( $deb\
+ug_lock)\n {\n my $g=new FileHandle;\n open\
+ ($g, \">>$fname\");\n print $g \"\\nDestroyed \
+by $$\\n\";\n close ($g);\n safe_system (\"m\
+v $fname $fname.old\");\n }\n else\n {\n \
+ unlink ($fname);\n }\n }\n return \"\";\n\
+ }\n \nsub file2string\n {\n my $file=@_[0];\n \
+ my $f=new FileHandle;\n my $r;\n open ($f, \"\
+$file\");\n while (<$f>){$r.=$_;}\n close ($f)\
+;\n return $r;\n }\nsub string2file \n {\n \
+ my ($s,$file,$mode)=@_;\n my $f=new FileHandle\
+;\n \n open ($f, \"$mode$file\");\n print\
+ $f \"$s\";\n close ($f);\n }\n\nBEGIN\n {\
+\n srand;\n \n $SIG{'SIGUP'}='signal_\
+cleanup';\n $SIG{'SIGINT'}='signal_cleanup';\\
+n $SIG{'SIGQUIT'}='signal_cleanup';\n $S\
+IG{'SIGILL'}='signal_cleanup';\n $SIG{'SIGTRA\
+P'}='signal_cleanup';\n $SIG{'SIGABRT'}='sign\
+al_cleanup';\n $SIG{'SIGEMT'}='signal_cleanup\
+';\n $SIG{'SIGFPE'}='signal_cleanup';\n \
+\n $SIG{'SIGKILL'}='signal_cleanup';\n $\
+SIG{'SIGPIPE'}='signal_cleanup';\n $SIG{'SIGS\
+TOP'}='signal_cleanup';\n $SIG{'SIGTTIN'}='si\
+gnal_cleanup';\n $SIG{'SIGXFSZ'}='signal_clea\
+nup';\n $SIG{'SIGINFO'}='signal_cleanup';\n \
+ \n $SIG{'SIGBUS'}='signal_cleanup';\n \
+ $SIG{'SIGALRM'}='signal_cleanup';\n $SIG{'S\
+IGTSTP'}='signal_cleanup';\n $SIG{'SIGTTOU'}=\
+'signal_cleanup';\n $SIG{'SIGVTALRM'}='signal\
+_cleanup';\n $SIG{'SIGUSR1'}='signal_cleanup'\
+;\n\n\n $SIG{'SIGSEGV'}='signal_cleanup';\n \
+ $SIG{'SIGTERM'}='signal_cleanup';\n $SIG{\
+'SIGCONT'}='signal_cleanup';\n $SIG{'SIGIO'}=\
+'signal_cleanup';\n $SIG{'SIGPROF'}='signal_c\
+leanup';\n $SIG{'SIGUSR2'}='signal_cleanup';\\
+n\n $SIG{'SIGSYS'}='signal_cleanup';\n $\
+SIG{'SIGURG'}='signal_cleanup';\n $SIG{'SIGCH\
+LD'}='signal_cleanup';\n $SIG{'SIGXCPU'}='sig\
+nal_cleanup';\n $SIG{'SIGWINCH'}='signal_clea\
+nup';\n \n $SIG{'INT'}='signal_cleanup';\
+\n $SIG{'TERM'}='signal_cleanup';\n $SIG\
+{'KILL'}='signal_cleanup';\n $SIG{'QUIT'}='si\
+gnal_cleanup';\n \n our $debug_lock=$ENV\
+{\"DEBUG_LOCK\"};\n \n \n \n \\
+n foreach my $a (@ARGV){$CL.=\" $a\";}\n \
+ if ( $debug_lock ){print STDERR \"\\n\\n\\n******\
+**** START PG: $PROGRAM *************\\n\";}\n \
+ if ( $debug_lock ){print STDERR \"\\n\\n\\n*****\
+*****(tcg) LOCKDIR: $LOCKDIR $$ *************\\n\"\
+;}\n if ( $debug_lock ){print STDERR \"\\n --\
+- $$ -- $CL\\n\";}\n \n \n \n \
+\n }\nsub flush_error\n {\n my $msg=shift;\\
+n return add_error ($EXIT_FAILURE,$$, $$,getppi\
+d(), $msg, $CL);\n }\nsub add_error \n {\n my\
+ $code=shift;\n my $rpid=shift;\n my $pid=sh\
+ift;\n my $ppid=shift;\n my $type=shift;\n \
+ my $com=shift;\n \n $ERROR_DONE=1;\n lo\
+ck4tc ($rpid, \"LERROR\",\"LSET\",\"$pid -- ERROR:\
+ $type\\n\");\n lock4tc ($$, \"LERROR\",\"LSET\\
+", \"$pid -- COM: $com\\n\");\n lock4tc ($$, \"\
+LERROR\",\"LSET\", \"$pid -- STACK: $ppid -> $pid\\
+\n\");\n \n return $code;\n }\nsub add_warni\
+ng \n {\n my $rpid=shift;\n my $pid =shift;\
+\n my $command=shift;\n my $msg=\"$$ -- WARN\
+ING: $command\\n\";\n print STDERR \"$msg\";\n \
+ lock4tc ($$, \"LWARNING\", \"LSET\", $msg);\n \
+}\n\nsub signal_cleanup\n {\n print dtderr \"\\
+\n**** $$ (tcg) was killed\\n\";\n &cleanup;\n \
+ exit ($EXIT_FAILURE);\n }\nsub clean_dir\n {\\
+n my $dir=@_[0];\n if ( !-d $dir){return ;}\\
+n elsif (!($dir=~/tmp/)){return ;}#safety check\
+ 1\n elsif (($dir=~/\\*/)){return ;}#safety che\
+ck 2\n else\n {\n `rm -rf $dir`;\n }\\
+n return;\n }\nsub cleanup\n {\n #print st\
+derr \"\\n----tc: $$ Kills $PIDCHILD\\n\";\n #k\
+ill (SIGTERM,$PIDCHILD);\n my $p=getppid();\n \
+ $CLEAN_EXIT_STARTED=1;\n \n \n \n if\
+ (&lock4tc($$,\"LERROR\", \"LCHECK\", \"\"))\n \
+ {\n my $ppid=getppid();\n if (!$ERROR_DONE) \n \
+ {\n &lock4tc($$,\"LERROR\", \"LSET\", \"$$ --\
+ STACK: $p -> $$\\n\");\n &lock4tc($$,\"LERROR\
+\", \"LSET\", \"$$ -- COM: $CL\\n\");\n }\n \
+ }\n my $warning=&lock4tc($$, \"LWARNING\", \"L\
+READ\", \"\");\n my $error=&lock4tc($$, \"LERR\
+OR\", \"LREAD\", \"\");\n #release error and wa\
+rning lock if root\n \n if (isrootpid() && (\
+$warning || $error) )\n {\n \n print STDERR \\
+"**************** Summary *************\\n$error\\\
+n$warning\\n\";\n\n &lock4tc($$,\"LERROR\",\"RELEA\
+SE\",\"\");\n &lock4tc($$,\"LWARNING\",\"RELEASE\"\
+,\"\");\n } \n \n \n foreach my $f (\
+@TMPFILE_LIST)\n {\n if (-e $f){unlink ($f);}\
+ \n }\n foreach my $d (@TMPDIR_LIST)\n \
+ {\n clean_dir ($d);\n }\n #No More Lock \
+Release\n #&lock4tc($$,\"LLOCK\",\"LRELEASE\",\\
+"\"); #release lock \n\n if ( $debug_lock ){pri\
+nt STDERR \"\\n\\n\\n********** END PG: $PROGRAM (\
+$$) *************\\n\";}\n if ( $debug_lock ){p\
+rint STDERR \"\\n\\n\\n**********(tcg) LOCKDIR: $L\
+OCKDIR $$ *************\\n\";}\n }\nEND \n {\n \
+ \n &cleanup();\n }\n \n\nsub safe_system \\
+n{\n my $com=shift;\n my $ntry=shift;\n my $ctr\
+y=shift;\n my $pid;\n my $status;\n my $ppid=ge\
+tppid();\n if ($com eq \"\"){return 1;}\n \n \n\
+\n if (($pid = fork ()) < 0){return (-1);}\n if \
+($pid == 0)\n {\n set_lock($$, \" -SHELL- \
+$com (tcg)\");\n exec ($com);\n }\n else\\
+n {\n lock4tc ($$, \"LLOCK\", \"LSET\", \"\
+$pid\\n\");#update parent\n $PIDCHILD=$pid;\n\
+ }\n if ($debug_lock){printf STDERR \"\\n\\t .\
+... safe_system (fasta_seq2hmm) p: $$ c: $pid COM\
+: $com\\n\";}\n\n waitpid ($pid,WTERMSIG);\n\n s\
+hift_lock ($pid,$$, \"LWARNING\",\"LWARNING\", \"L\
+SET\");\n\n if ($? == $EXIT_FAILURE || lock4tc($p\
+id, \"LERROR\", \"LCHECK\", \"\"))\n {\n i\
+f ($ntry && $ctry <$ntry)\n {\n add_warning ($$,\
+$$,\"$com failed [retry: $ctry]\");\n lock4tc ($\
+pid, \"LRELEASE\", \"LERROR\", \"\");\n return s\
+afe_system ($com, $ntry, ++$ctry);\n }\n elsi\
+f ($ntry == -1)\n {\n if (!shift_lock ($pid, $$,\
+ \"LERROR\", \"LWARNING\", \"LSET\"))\n {\n \
+ add_warning ($$,$$,\"$com failed\");\n }\n\
+ else\n {\n lock4tc ($pid, \"LRELEASE\\
+", \"LERROR\", \"\");\n }\n return $?;}\n \
+ else\n {\n if (!shift_lock ($pid,$$, \"LERROR\
+\",\"LERROR\", \"LSET\"))\n {\n myexit(a\
+dd_error ($EXIT_FAILURE,$$,$pid,getppid(), \"UNSPE\
+CIFIED system\", $com));\n }\n }\n }\n ret\
+urn $?;\n}\n\nsub check_configuration \n {\n \
+ my @l=@_;\n my $v;\n foreach my $p (@\
+l)\n {\n \n if ( $p eq \"EMAIL\")\n { \n\
+ if ( !($EMAIL=~/@/))\n {\n add_warning($$\
+,$$,\"Could Not Use EMAIL\");\n myexit(add_error \
+($EXIT_FAILURE,$$,$$,getppid(),\"EMAIL\",\"$CL\"))\
+;\n }\n }\n elsif( $p eq \"INTERNET\")\
+\n {\n if ( !&check_internet_connection(\
+))\n {\n myexit(add_error ($EXIT_FAILURE,$$,$$\
+,getppid(),\"INTERNET\",\"$CL\"));\n }\n }\n \
+ elsif( $p eq \"wget\")\n {\n if (!&pg_\
+is_installed (\"wget\") && !&pg_is_installed (\"cu\
+rl\"))\n {\n myexit(add_error ($EXIT_FAILURE,$\
+$,$$,getppid(),\"PG_NOT_INSTALLED:wget\",\"$CL\"))\
+;\n }\n }\n elsif( !(&pg_is_installed ($p))\
+)\n {\n myexit(add_error ($EXIT_FAILURE,\
+$$,$$,getppid(),\"PG_NOT_INSTALLED:$p\",\"$CL\"));\
+\n }\n }\n return 1;\n }\nsub pg_is_in\
+stalled\n {\n my @ml=@_;\n my $r, $p, $m;\n\
+ my $supported=0;\n \n my $p=shift (@ml);\
+\n if ($p=~/::/)\n {\n if (safe_system (\"\
+perl -M$p -e 1\")==$EXIT_SUCCESS){return 1;}\n els\
+e {return 0;}\n }\n else\n {\n $r=`wh\
+ich $p 2>/dev/null`;\n if ($r eq \"\"){return 0;}\\
+n else {return 1;}\n }\n }\n\n\n\nsub check_\
+internet_connection\n {\n my $internet;\n m\
+y $tmp;\n &check_configuration ( \"wget\"); \n \
+ \n $tmp=&vtmpnam ();\n \n if (&pg_\
+is_installed (\"wget\")){`wget www.google.com -\
+O$tmp >/dev/null 2>/dev/null`;}\n elsif (&pg_i\
+s_installed (\"curl\")){`curl www.google.com -o\
+$tmp >/dev/null 2>/dev/null`;}\n \n if ( !-e\
+ $tmp || -s $tmp < 10){$internet=0;}\n else {$i\
+nternet=1;}\n if (-e $tmp){unlink $tmp;}\n\n \
+ return $internet;\n }\nsub check_pg_is_installed\
+\n {\n my @ml=@_;\n my $r=&pg_is_installed \
+(@ml);\n if (!$r && $p=~/::/)\n {\n print \
+STDERR \"\\nYou Must Install the perl package $p o\
+n your system.\\nRUN:\\n\\tsudo perl -MCPAN -e 'in\
+stall $pg'\\n\";\n }\n elsif (!$r)\n \
+{\n myexit(flush_error(\"\\nProgram $p Supported b\
+ut Not Installed on your system\"));\n }\n \
+ else\n {\n return 1;\n }\n }\n\n\n","u\
+se Cwd;\nuse Env;\nuse File::Path;\nuse FileHandle\
+;\nuse strict;\n\n\nour (%MODE, %PG, %ENV_SET, %SU\
+PPORTED_OS);\n\n\nour $EXIT_SUCCESS=0;\nour $EXIT_\
+FAILURE=1;\nour $INTERNET=0;\n\nour $CP=\"cp \"; #\
+was causing a crash on MacOSX\nour $SILENT=\">/dev\
+/null 2>/dev/null\";\nour $WEB_BASE=\"http://www.t\
+coffee.org\";\nour $TCLINKDB_ADDRESS=\"$WEB_BASE/R\
+esources/tclinkdb.txt\";\nour $OS=get_os();\nour $\
+ROOT=&get_root();\nour $CD=cwd();\nour $CDIR=$CD;\\
+nour $HOME=$ENV{'HOME'};\n\nour $OSNAME=$ENV{'OSNA\
+ME'};\nour $OSARCH=$ENV{'OSARCH'};\nour $REPO_ROOT\
+=\"\";\n\nour $TCDIR;\nour $TCCACHE;\nour $TCTMP;\\
+nour $TCM;\nour $TCMETHODS;\nour $TCPLUGINS;\nour \
+$PLUGINS_DIR=\"\";\nour $INSTALL_DIR=\"\";\n\nour \
+$CXX=\"g++\";\nour $CXXFLAGS=\"\";\n\nour $CPP=\"g\
+++\";\nour $CPPFLAGS=\"\";\n\nour $CC=\"gcc\";\nou\
+r $CFLAGS=\"\";\n\nour $FC=\"f77\";\nour $FFLAGS=\\
+"\";\n\nmy $install=\"all\";\nmy $default_update_a\
+ction=\"no_update\";\nmy @required_applications=(\\
+"wget_OR_curl\");\nmy @smode=(\"all\", \"clean\", \
+\"install\");\n\n&initialize_PG();\n\nmy $cl=join(\
+ \" \", @ARGV);\nif ($#ARGV==-1 || ($cl=~/-h/) ||(\
+$cl=~/-H/) )\n {\n print \"\\n!!!!!!! ./insta\
+ll t_coffee --> installs t_coffee onl\
+y\";\n print \"\\n!!!!!!! ./install all \
+ --> installs all the modes [mcoffee, e\
+xpresso, psicoffee,rcoffee..]\";\n print \"\\n\
+!!!!!!! ./install [mcoffee|rcoffee|..] --> instal\
+ls the specified mode\";\n print \"\\n!!!!!!! \
+./install -h --> print usage\\n\
+\\n\";\n if ( $#ARGV==-1){exit ($EXIT_FAILURE)\
+;}\n }\n \nif (($cl=~/-h/) ||($cl=~/-H/) )\n\
+ {\n my $m;\n print \"\\n\\n!!!!!!! advance\
+d mode\\n\";\n foreach $m ((keys (%MODE)),@smod\
+e)\n {\n print \"!!!!!!! ./install $m\\\
+n\";\n }\n \n print \"!!!!!!! ./install\
+ [target:package|mode|] [-update|-force|-exec=dir|\
+-dis=dir|-root|-tclinkdb=file|-] [CC=|FCC=|CXX=|CF\
+LAGS=|CXXFLAGS=]\\n\";\n print \"!!!!!!! ./inst\
+all clean [removes all executables]\\n\";\n \
+print \"!!!!!!! ./install [optional:target] -updat\
+e [updates package already installed\
+]\\n\";\n print \"!!!!!!! ./install [optional:t\
+arget] -force [Forces recompilation\
+ over everything]\\n\";\n \n print \"!!!!!!!\
+ ./install [optional:target] -root \
+ [You are running as root]\\n\";\n print \"!!!!\
+!!! ./install [optional:target] -exec=/foo/bar/ \
+ [address for the T-Coffee executable]\\n\";\n \
+ print \"!!!!!!! ./install [optional:target] -di\
+s=/foo/bar/ [Address where distributions sh\
+ould be stored]\\n\";\n print \"!!!!!!! ./insta\
+ll [optional:target] -tclinkdb=foo|update [file c\
+ontaining all the packages to be installed]\\n\";\\
+n print \"!!!!!!! ./install [optional:target] -\
+clean [clean everything]\\n\";\n \
+ print \"!!!!!!! ./install [optional:target] -plug\
+ins [plugins directory]\\n\";\n pr\
+int \"!!!!!!! ./install [optional:target] -tcdir=/\
+foor/bar [base path where T-Coffee will be in\
+stalled]\\n\";\n print \"!!!!!!! ./install [opt\
+ional:target] -repo=/path/to/repo [binaries repo\
+sitory root directory]\\n\";\n print \"!!!!!!! \
+mode:\";\n foreach $m (keys(%MODE)){print \"$m \
+\";}\n print \"\\n\";\n print \"!!!!!!! Pack\
+ages:\";\n foreach $m (keys (%PG)){print \"$m \\
+";}\n print \"\\n\";\n \n print \"\\n\\n\\
+";\n exit ($EXIT_FAILURE);\n }\n\n\n\nmy (@arg\
+l)=($cl=~/(\\S+=[^=]+)\\s\\w+=/g);\npush (@argl, (\
+$cl=~/(\\S+=[^=]+\\S)\\s*$/g));\n\nforeach $a (@ar\
+gl)\n {\n if ( ($cl=~/CXX=(.*)/)){$CXX=$1;}\n \
+ if ( ($cl=~/-CC=(.*)/ )){$CC=$1;}\n if ( \
+($cl=~/-FC=(.*)/ )){$FC=$1;}\n if ( ($cl=~/-\
+CFLAGS=(.*)/)){$CFLAGS=$1;}\n if ( ($cl=~/-CXXF\
+LAGS=(.*)/)){$CXXFLAGS=$1;}\n }\nour ($ROOT_INSTA\
+LL, $NO_QUESTION, $default_update_action,$BINARIES\
+_ONLY,$force, $default_update_action, $INSTALL_DIR\
+, $PLUGINS_DIR, $DISTRIBUTIONS,$tclinkdb, $proxy, \
+$clean);\nif ( ($cl=~/-root/)){$ROOT_INSTALL=1;}\n\
+if ( ($cl=~/-no_question/)){$NO_QUESTION=1;}\nif (\
+ ($cl=~/-update/)){$default_update_action=\"update\
+\";}\nif ( ($cl=~/-binaries/)){$BINARIES_ONLY=1;}\\
+nif ( ($cl=~/-force/)){$force=1;$default_update_ac\
+tion=\"update\"}\nif ( ($cl=~/-exec=\\s*(\\S+)/)){\
+$INSTALL_DIR=$1;}\nif ( ($cl=~/-plugins=\\s*(\\S+)\
+/)){$PLUGINS_DIR=$1;}\nif ( ($cl=~/-dis=\\s*(\\S+)\
+/)){$DISTRIBUTIONS=$1;}\n\nif ( ($cl=~/-tclinkdb=\\
+\s*(\\S+)/)){$tclinkdb=$1;}\nif ( ($cl=~/-proxy=\\\
+s*(\\S+)/)){$proxy=$1;}\nif ( ($cl=~/-clean/)){$cl\
+ean=1;}\nif ( ($cl=~/-repo=\\s*(\\S+)/)){ $REPO_RO\
+OT=$1; }\nif ( ($cl=~/-tcdir=\\s*(\\S+)/)){ $TCDIR\
+=$1; }\nif ($tclinkdb){&update_tclinkdb ($tclinkdb\
+);}\n\n\nif( $REPO_ROOT ne \"\" ) {\n if( $OSNAME \
+eq \"\" ) { print \"You have specified the reposit\
+ory folder but the required \\\"OSNAME\\\" envirom\
+ent variable is missing. \\n\"; exit 1; } \n if( $\
+OSARCH eq \"\" ) { print \"You have specified the \
+repository folder but the required \\\"OSARCH\\\" \
+enviroment variable is missing. \\n\"; exit 1; } \\
+n}\n\n\nif(!$TCDIR) { $TCDIR=\"$HOME/.t_coffee\"; \
+}\n&add_dir ($TCDIR);\n&add_dir ($TCCACHE=\"$TCDIR\
+/cache\");\n&add_dir ($TCTMP=\"$CDIR/tmp\");\n&add\
+_dir ($TCM=\"$TCDIR/mcoffee\");\n&add_dir ($TCMETH\
+ODS=\"$TCDIR/methods\");\n&add_dir ($TCPLUGINS=\"$\
+TCDIR/plugins/$OS\");\n\n\nour $BASE=\"$CD/bin\";\\
+nour $BIN=\"$BASE/binaries/$OS\";\nour $DOWNLOAD_D\
+IR=\"$BASE/download\";\nour $DOWNLOAD_FILE=\"$DOWN\
+LOAD_DIR/files\";\nour $TMP=\"$BASE/tmp\";\n\n&add\
+_dir($BASE);\n&add_dir($BIN);\n&add_dir($DOWNLOAD_\
+DIR);\n&add_dir($DOWNLOAD_FILE);\nif (!$DISTRIBUTI\
+ONS){$DISTRIBUTIONS=\"$DOWNLOAD_DIR/distributions\\
+";}\n&add_dir ($DISTRIBUTIONS);\n&add_dir ($TMP);\\
+n\n\nif (!$PLUGINS_DIR && !$ROOT_INSTALL){$PLUG\
+INS_DIR=$TCPLUGINS;}\nelsif (!$PLUGINS_DIR && $RO\
+OT_INSTALL){$PLUGINS_DIR=\"/usr/local/bin/\";}\n\n\
+if (!$INSTALL_DIR && !$ROOT_INSTALL){$INSTALL_D\
+IR=\"$HOME/bin/\";mkpath ($INSTALL_DIR);}\nelsif (\
+!$INSTALL_DIR && $ROOT_INSTALL){$INSTALL_DIR=\"/u\
+sr/local/bin/\";}\n\nif (-d \"mcoffee\"){`cp mcoff\
+ee/* $TCM`;}\n\n\nour $ENV_FILE=\"$TCDIR/t_coffee_\
+env\";\n&env_file2putenv ($ENV_FILE);\n&set_proxy(\
+$proxy);\nmy ($target, $p, $r);\n$target=$p;\n\nfo\
+reach $p ( ((keys (%PG)),(keys(%MODE)),(@smode)) \
+)\n {\n if ($ARGV[0] eq $p && $target eq \"\")\
+{$target=$p;}\n }\nif ($target eq \"\"){exit ($EX\
+IT_FAILURE);}\n\n\nforeach $r (@required_applicati\
+ons)\n {\n my @app_list;\n my $i;\n $i=0\
+;\n \n @app_list=split (/_OR_/, $r);\n fo\
+reach my $pg (@app_list)\n {\n $i+=&pg_is_ins\
+talled ($pg);\n }\n if ($i==0)\n {\n \
+ print \"One of the following packages must be\
+ installed to proceed: \";\n foreach my $pg (\
+@app_list)\n {\n print (\"$pg \");\n }\n di\
+e;\n }\n }\n\n\n\n\n\n\n&sign_license_ni();\n\\
+n\n$PG{C}{compiler}=get_C_compiler($CC);\n$PG{Fort\
+ran}{compiler}=get_F_compiler($FC);\n$PG{CXX}{comp\
+iler}=$PG{CPP}{compiler}=$PG{GPP}{compiler}=get_CX\
+X_compiler($CXX);\nif ($CXXFLAGS){$PG{CPP}{options\
+}=$PG{GPP}{options}=$PG{CXX}{options}=$CXXFLAGS;}\\
+nif ($CFLAGS){$PG{C}{options}=$CFLAGS;}\nforeach m\
+y $c (keys(%PG))\n {\n my $arguments;\n if \
+($PG{$c}{compiler})\n {\n $arguments=\"$PG{$c\
+}{compiler_flag}=$PG{$c}{compiler} \";\n if ($PG{$\
+c}{options})\n {\n $arguments.=\"$PG{$c}{opt\
+ions_flag}=$PG{$c}{options} \";\n }\n $PG{$c}{ar\
+guments}=$arguments;\n }\n }\n\nif ($PG{$tar\
+get}){$PG{$target}{install}=1;}\nelse\n {\n fo\
+reach my $pg (keys(%PG))\n {\n if ( $target e\
+q \"all\" || ($PG{$pg}{mode}=~/$target/))\n {\n \
+ $PG{$pg} {install}=1;\n }\n }\n }\n\nf\
+oreach my $pg (keys(%PG))\n {\n if (!$PG{$pg}{\
+update_action}){$PG{$pg}{update_action}=$default_u\
+pdate_action;}\n elsif ($PG{$pg}{update_action}\
+ eq \"never\"){$PG{$pg}{install}=0;}\n if ( $fo\
+rce && $PG{$pg}{install})\n {\n `rm $BIN/$pg \
+$BIN/$pg.exe $SILENT`;\n }\n if ($PG{$pg}{\
+update_action} eq \"update\" && $PG{$pg}{install})\
+{$PG{$pg}{update}=1;}\n }\n\nif (($target=~/clean\
+/))\n {\n print \"------- cleaning executables\
+ -----\\n\";\n `rm bin/* $SILENT`;\n exit ($\
+EXIT_SUCCESS);\n }\n\nif ( !$PG{$target}){print \\
+"------- Installing T-Coffee Modes\\n\";}\n\nforea\
+ch my $m (keys(%MODE))\n {\n if ( $target eq \\
+"all\" || $target eq $m)\n {\n print \"\\n---\
+---- The installer will now install the $m compone\
+nts $MODE{$m}{description}\\n\";\n foreach my $pg \
+(keys(%PG))\n {\n if ( $PG{$pg}{mode} =~/$m/\
+ && $PG{$pg}{install})\n {\n if ($PG{$pg}{t\
+ouched}){print \"------- $PG{$pg}{dname}: already \
+processed\\n\";}\n else {$PG{$pg}{success}=&insta\
+ll_pg($pg);$PG{$pg}{touched}=1;}\n }\n }\n\
+ }\n }\n\nif ( $PG{$target}){print \"-------\
+ Installing Individual Package\\n\";}\nforeach my \
+$pg (keys (%PG))\n {\n \n if ( $PG{$pg}{ins\
+tall} && !$PG{$pg}{touched})\n {\n print \"\\\
+n------- Install $pg\\n\";\n $PG{$pg}{success}=&in\
+stall_pg($pg);$PG{$pg}{touched}=1;\n }\n }\n\
+print \"------- Finishing The installation\\n\";\n\
+my $final_report=&install ($INSTALL_DIR);\n\nprint\
+ \"\\n\";\nprint \"*******************************\
+**************************************\\n\";\nprin\
+t \"******** INSTALLATION SUMMARY \
+ *****************\\n\";\nprint \"***********\
+**************************************************\
+********\\n\";\nprint \"------- SUMMARY package In\
+stallation:\\n\";\nprint \"------- Executable In\
+stalled in: $PLUGINS_DIR\\n\";\n\nforeach my $pg (\
+keys(%PG))\n {\n if ( $PG{$pg}{install})\n \
+ {\n my $bin_status=($PG{$pg}{from_binary} && $PG\
+{$pg}{success})?\"[from binary]\":\"\";\n if (\
+ $PG{$pg}{new} && !$PG{$pg}{old}) \
+ {print \"*------ $PG{$pg}{dname}: insta\
+lled $bin_status\\n\"; $PG{$pg}{status}=1;}\n elsi\
+f ( $PG{$pg}{new} && $PG{$pg}{old}) \
+ {print \"*------ $PG{$pg}{dname}: u\
+pdated $bin_status\\n\" ; $PG{$pg}{status}=1;} \n\
+ elsif (!$PG{$pg}{new} && $PG{$pg}{old} && !$PG{\
+$pg}{update}){print \"*------ $PG{$pg}{dnam\
+e}: previous\\n\" ; $PG{$pg}{status}=1;}\n elsif \
+(!$PG{$pg}{new} && $PG{$pg}{old} && $PG{$pg}{upd\
+ate}){print \"*------ $PG{$pg}{dname}: fail\
+ed update (previous installation available)\\n\";$\
+PG{$pg}{status}=0;}\n else \
+ {print \"*------\
+ $PG{$pg}{dname}: failed installation\\n\";\
+$PG{$pg}{status}=0;}\n }\n }\nmy $failure;\n\
+\nif ( !$PG{$target}){print \"*------ SUMMARY mode\
+ Installation:\\n\";}\nforeach my $m (keys(%MODE))\
+\n {\n \n if ( $target eq \"all\" || $target \
+eq $m)\n {\n my $succesful=1;\n foreach my $p\
+g (keys(%PG))\n {\n if (($PG{$pg}{mode}=~/$m\
+/) && $PG{$pg}{install} && $PG{$pg}{status}==0)\n \
+ {\n $succesful=0;\n print \"*!!!!!! \
+$PG{$pg}{dname}: Missing\\n\";\n }\n }\n i\
+f ( $succesful)\n {\n $MODE{$m}{status}=1;\n\
+ print \"*------ MODE $MODE{$m}{dname} S\
+UCCESSFULLY installed\\n\";\n }\n else\n {\n \
+ $failure++;\n $MODE{$m}{status}=0;\n pr\
+int \"*!!!!!! MODE $MODE{$m}{dname} UNSUCCES\
+SFULLY installed\\n\";\n }\n }\n }\n\n \
+\n \nif ($clean==1 && ($BASE=~/install4tcoffe\
+e/) ){print \"*------ Clean Installation Directory\
+: $BASE\\n\";`rm -rf $BASE`;}\nforeach my $pg (key\
+s(%PG)){if ($PG{$pg}{install} && $PG{$pg}{status}=\
+=0){exit ($EXIT_FAILURE);}}\n\nif ($failure)\n {\\
+n print \"*************************************\
+********************************\\n\";\n print \
+\"******** SOME PACKAGES FAILED TO INSTALL \
+ *****************\\n\";\n print \"*********\
+**************************************************\
+**********\\n\";\n print \"\\nSome of the repor\
+ted failures may be due to connectivity problems\"\
+;\n print \"\\nRerun the installation and the i\
+nstaller will specifically try to install the miss\
+ing packages\";\n print \"\\nIf this Fails, go \
+to the original website and install the package ma\
+nually\";\n }\n\nprint \"************************\
+*********************************************\\n\"\
+;\nprint \"******** FINALIZE YOUR INS\
+TALLATION *****************\\n\";\nprint \"****\
+**************************************************\
+***************\\n\";\nprint \"------- Your execut\
+ables are in:\\n\"; \nprint \"------- $PLUGI\
+NS_DIR:\\n\";\nprint \"------- Add this directory \
+to your path with the following command:\\n\";\npr\
+int \"------- export PATH=$PLUGINS_DIR:\\$PA\
+TH\\n\";\nprint \"------- Make this permanent by a\
+dding this line to the file:\\n\";\nprint \"------\
+- $HOME/.bashrc\\n\";\nexit ($EXIT_SUCCESS);\
+ \n \nsub get_CXX_compiler\n {\n my $c=@_[0]\
+;\n my (@clist)=(\"g++\");\n \n return ge\
+t_compil ($c, @clist);\n }\nsub get_C_compiler\n \
+{\n my $c=@_[0];\n my (@clist)=(\"gcc\", \"c\
+c\", \"icc\");\n \n return get_compil ($c, @\
+clist);\n }\n\nsub get_F_compiler\n {\n my ($c\
+)=@_[0];\n my @clist=(\"f77\", \"g77\",\"g95\",\
+ \"gfortran\", \"ifort\");\n return get_compil \
+($c, @clist);\n } \n \nsub get_compil\n {\\
+n my ($fav,@clist)=(@_);\n \n #return the\
+ first compiler found installed in the system. Che\
+ck first the favorite\n foreach my $c ($fav,@cl\
+ist)\n {\n if (&pg_is_installed ($c)){return\
+ $c;}\n }\n return \"\";\n }\nsub exit_if\
+_pg_not_installed\n {\n my (@arg)=(@_);\n \\
+n foreach my $p (@arg)\n {\n if ( !&pg_is_\
+installed ($p))\n {\n print \"!!!!!!!! The $\
+p utility must be installed for this installation \
+to proceed [FATAL]\\n\";\n die;\n }\n }\
+\n return 1;\n }\nsub set_proxy\n {\n my (\
+$proxy)=(@_);\n my (@list,$p);\n \n @list\
+= (\"HTTP_proxy\", \"http_proxy\", \"HTTP_PROXY\",\
+ \"ALL_proxy\", \"all_proxy\",\"HTTP_proxy_4_TCOFF\
+EE\",\"http_proxy_4_TCOFFEE\");\n \n if (!$p\
+roxy)\n {\n foreach my $p (@list)\n {\n \
+ if ( ($ENV_SET{$p}) || $ENV{$p}){$proxy=$ENV{$p};\
+}\n }\n }\n foreach my $p(@list){$ENV{$p\
+}=$proxy;}\n }\n \nsub check_internet_connection\\
+n {\n my $internet;\n \n if ( -e \"x\"){\
+unlink (\"x\");}\n if (&pg_is_installed \
+(\"wget\")){`wget www.google.com -Ox >/dev/null 2>\
+/dev/null`;}\n elsif (&pg_is_installed (\"c\
+url\")){`curl www.google.com -ox >/dev/null 2>/dev\
+/null`;}\n else\n {\n printf stderr \"\\nE\
+RROR: No pg for remote file fetching [wget or curl\
+][FATAL]\\n\";\n exit ($EXIT_FAILURE);\n }\n \
+ \n if ( !-e \"x\" || -s \"x\" < 10){$interne\
+t=0;}\n else {$internet=1;}\n if (-e \"x\"){\
+unlink \"x\";}\n return $internet;\n }\nsub ur\
+l2file\n {\n my ($cmd, $file,$wget_arg, $curl_\
+arg)=(@_);\n my ($exit,$flag, $pg, $arg);\n \
+\n if ($INTERNET || check_internet_connection (\
+)){$INTERNET=1;}\n else\n {\n print STDERR\
+ \"ERROR: No Internet Connection [FATAL:install.pl\
+]\\n\";\n exit ($EXIT_FAILURE);\n }\n \n \
+ if (&pg_is_installed (\"wget\")){$pg=\"wg\
+et\"; $flag=\"-O\";$arg=\"--tries=2 --connect-time\
+out=10 $wget_arg\";}\n elsif (&pg_is_installed\
+ (\"curl\")){$pg=\"curl\"; $flag=\"-o\";$arg=$c\
+url_arg;}\n else\n {\n printf stderr \"\\n\
+ERROR: No pg for remote file fetching [wget or cur\
+l][FATAL]\\n\";\n exit ($EXIT_FAILURE);\n }\n\
+ \n \n if (-e $file){unlink($file);}\n \
+ $exit=system \"$pg $cmd $flag$file $arg\";\n r\
+eturn $exit;\n }\n\nsub pg_is_installed\n {\n \
+ my ($p, $dir)=(@_);\n my ($r,$m, $ret);\n m\
+y ($supported, $language, $compil);\n \n \n \
+ if ( $PG{$p})\n {\n $language=$PG{$p}{langua\
+ge2};\n $compil=$PG{$language}{compiler};\n }\
+\n \n if ( $compil eq \"CPAN\")\n {\n i\
+f ( system (\"perl -M$p -e 1\")==$EXIT_SUCCESS){$r\
+et=1;}\n else {$ret=0;}\n }\n elsif ($dir)\
+\n {\n if (-e \"$dir/$p\" || -e \"$dir/$p\\.e\
+xe\"){$ret=1;}\n else {$ret=0;}\n }\n elsi\
+f (-e \"$PLUGINS_DIR/$p\" || -e \"$PLUGINS_DIR/$p.\
+exe\"){$ret=1;}\n else\n {\n $r=`which $p \
+2>/dev/null`;\n if ($r eq \"\"){$ret=0;}\n else {$\
+ret=1;}\n }\n \n return $ret;\n }\nsub \
+install\n {\n my ($new_bin)=(@_);\n my ($co\
+pied, $report);\n\n \n if (!$ROOT_INSTALL)\n\
+ {\n \n if (-e \"$BIN/t_coffee\"){`$CP $BIN/t\
+_coffee $INSTALL_DIR`};\n `cp $BIN/* $PLUGINS_DIR`\
+;\n $copied=1;\n }\n else\n {\n $copi\
+ed=&root_run (\"You must be root to finalize the i\
+nstallation\", \"$CP $BIN/* $INSTALL_DIR $SILENT\"\
+);\n }\n \n \n if ( !$copied)\n {\\
+n $report=\"*!!!!!! Installation unsuccesful.\
+ The executables have been left in $BASE/bin\\n\";\
+\n }\n elsif ( $copied && $ROOT)\n {\n \
+ $report=\"*------ Installation succesful. Your ex\
+ecutables have been copied in $new_bin and are on \
+your PATH\\n\";\n }\n elsif ( $copied && !$ROO\
+T)\n {\n $report= \"*!!!!!! T-Coffee and a\
+ssociated packages have been copied in: $new_bin\\\
+n\";\n $report.=\"*!!!!!! This address is NOT\
+ in your PATH sytem variable\\n\";\n $report.\
+=\"*!!!!!! You can do so by adding the following l\
+ine in your ~/.bashrc file:\\n\";\n $report.=\
+\"*!!!!!! export PATH=$new_bin:\\$PATH\\n\";\n \
+}\n return $report;\n}\n\nsub sign_license_ni\n \
+{\n my $F=new FileHandle;\n open ($F, \"lice\
+nse.txt\");\n while (<$F>)\n {\n print \"$\
+_\";\n }\n close ($F);\n \n return;\\
+n }\n\nsub install_pg\n {\n my ($pg)=(@_);\n \
+ my ($report, $previous, $language, $compiler, $\
+return);\n \n if (!$PG{$pg}{install}){return\
+ 1;}\n \n $previous=&pg_is_installed ($pg);\\
+n \n if ($PG{$pg}{update_action} eq \"no_upd\
+ate\" && $previous)\n {\n $PG{$pg}{old}=1;\n \
+$PG{$pg}{new}=0;\n $return=1;\n }\n else\n\
+ {\n $PG{$pg}{old}=$previous;\n \n if ($PG{$p\
+g} {language2} eq \"Perl\"){&install_perl_package \
+($pg);}\n elsif ($BINARIES_ONLY && &install_binary\
+_package ($pg)){$PG{$pg}{from_binary}=1;}\n elsif \
+(&install_source_package ($pg)){;}\n else \n {\n\
+ \n if (!&supported_os($OS))\n {\n \
+print \"!!!!!!!! $pg compilation failed, binary un\
+supported for $OS\\n\"; \n }\n elsif (!(\
+$PG{$pg}{from_binary}=&install_binary_package ($pg\
+)))\n {\n print \"!!!!!!!! $pg compilation \
+and binary installation failed\\n\";\n }\n \
+ }\n $PG{$pg}{new}=$return=&pg_is_installed ($pg,\
+$BIN);\n }\n\n \n return $return;\n }\\
+nsub install_perl_package\n {\n my ($pg)=(@_);\
+\n my ($report, $language, $compiler);\n \n \
+ $language=$PG{$pg} {language2};\n $compiler=\
+$PG{$language}{compiler};\n \n if (!&pg_is_i\
+nstalled ($pg))\n {\n if ( $OS eq \"windows\"\
+){`perl -M$compiler -e 'install $pg'`;}\n elsif ( \
+$ROOT eq \"sudo\"){system (\"sudo perl -M$compiler\
+ -e 'install $pg'\");}\n else {system (\"su root -\
+c perl -M$compiler -e 'install $pg'\");}\n }\\
+n return &pg_is_installed ($pg);\n }\n\n\n\nsu\
+b install_source_package\n {\n my ($pg)=(@_);\\
+n my ($report, $download, $arguments, $language\
+, $address, $name, $ext, $main_dir, $distrib);\n \
+ my $wget_tmp=\"$TMP/wget.tmp\";\n my (@fl);\n\
+ if ( -e \"$BIN/$pg\" || -e \"$BIN/$pg.exe\"){r\
+eturn 1;}\n \n #\n # check if the module \
+exists in the repository cache \n #\n if( repo_\
+load($pg) ) {\n return 1;\n }\n \n if ($pg \
+eq \"t_coffee\") {return &install_t_coffee ($pg\
+);}\n elsif ($pg eq \"TMalign\"){return &inst\
+all_TMalign ($pg);}\n \n chdir $DISTRIBUTION\
+S;\n \n $download=$PG{$pg}{source};\n \n \
+ if (($download =~/tgz/))\n {\n ($address,$\
+name,$ext)=($download=~/(.+\\/)([^\\/]+)(\\.tgz).*\
+/);\n }\n elsif (($download=~/tar\\.gz/))\\
+n {\n ($address,$name,$ext)=($download=~/(.+\\
+\/)([^\\/]+)(\\.tar\\.gz).*/);\n }\n elsif\
+ (($download=~/tar/))\n {\n ($address,$name,$\
+ext)=($download=~/(.+\\/)([^\\/]+)(\\.tar).*/);\n \
+ }\n else\n {\n ($address,$name)=($dow\
+nload=~/(.+\\/)([^\\/]+)/);\n $ext=\"\";\n }\\
+n $distrib=\"$name$ext\";\n \n if ( !-d $\
+pg){mkdir $pg;}\n chdir $pg;\n \n #get the\
+ distribution if available\n if ( -e \"$DOWNLOA\
+D_DIR/$distrib\")\n {\n `$CP $DOWNLOAD_DIR/$d\
+istrib .`;\n }\n #UNTAR and Prepare everyt\
+hing\n if (!-e \"$name.tar\" && !-e \"$name\")\\
+n {\n &check_rm ($wget_tmp);\n print \"\\n---\
+---- Downloading/Installing $pg\\n\";\n \n if (!-e\
+ $distrib && &url2file (\"$download\", \"$wget_tmp\
+\")==$EXIT_SUCCESS)\n {\n \n `mv $wget_t\
+mp $distrib`;\n `$CP $distrib $DOWNLOAD_DIR/`;\
+\n }\n\n if (!-e $distrib)\n {\n print \"!\
+!!!!!! Download of $pg distribution failed\\n\";\n\
+ print \"!!!!!!! Check Address: $PG{$pg}{sourc\
+e}\\n\";\n return 0;\n }\n print \"\\n------\
+- unzipping/untaring $name\\n\";\n if (($ext =~/z/\
+))\n { \n &flush_command (\"gunzip $name$ext\
+\");\n \n }\n if (($ext =~/tar/) || ($ext =~\
+/tgz/))\n {\n &flush_command(\"tar -xvf $nam\
+e.tar\");\n }\n }\n #Guess and enter the\
+ distribution directory\n @fl=ls($p);\n fore\
+ach my $f (@fl)\n {\n if (-d $f)\n {\n \
+$main_dir=$f;\n }\n }\n if (-d $main_dir\
+)\n \n {\n chdir $main_dir;}\n else\n \
+ {\n print \"Error: $main_dir does not exist\";\\
+n }\n print \"\\n------- Compiling/Install\
+ing $pg\\n\";\n `make clean $SILENT`;\n \n \
+ \n #\n # SAP module\n #\n if ($pg eq\
+ \"sap\")\n {\n if (-e \"./configure\")\n {\
+\n #new sap distribution\n if ($OS eq \"ma\
+cosx\")\n {\n &replace_line_in_file (\"./sr\
+c/galloc.h\", \"malloc.h\", \"\");\n &replace_li\
+ne_in_file (\"./src/pdbprot.h\", \"malloc.h\", \"\\
+");\n &replace_line_in_file (\"./src/pdbprot.c\",\
+ \"malloc.h\", \"\");\n }\n \n &flus\
+h_command (\"./configure\");\n &flush_command \
+(\"make clean\");\n &flush_command (\"make\");\
+\n &check_cp (\"./src/$pg\", \"$BIN\");\n \
+repo_store(\"./src/$pg\");\n }\n else\n {\n \
+ #old style distribution\n `rm *.o sap sap.e\
+xe ./util/aa/*.o ./util/wt/.o $SILENT`;\n &fl\
+ush_command (\"make $arguments sap\");\n &chec\
+k_cp ($pg, \"$BIN\");\n repo_store($pg);\n }\
+\n }\n \n #\n # CLUSTALW2 module\n \
+ #\n elsif ($pg eq \"clustalw2\")\n {\n &\
+flush_command(\"./configure\");\n &flush_command(\\
+"make $arguments\");\n &check_cp (\"./src/$pg\", \\
+"$BIN\");\n repo_store(\"./src/$pg\");\n }\n \
+ \n #\n # FSA module\n # \n elsif ($\
+pg eq \"fsa\")\n {\n &flush_command(\"./confi\
+gure --prefix=$BIN\");\n &flush_command(\"make $ar\
+guments\");\n &flush_command (\"make install\");\n\
+\n repo_store(\"fsa\", \"$BIN/bin\");\n `mv $BIN/b\
+in/* $BIN`;\n `rmdir $BIN/bin`;\n }\n \n \
+ #\n # CLUSTALW module\n #\n elsif ($pg \
+eq \"clustalw\")\n {\n &flush_command(\"make \
+$arguments clustalw\");\n `$CP $pg $BIN $SILENT`;\\
+n repo_store($pg);\n }\n \n #\n # MA\
+FFT module\n #\n elsif ($pg eq \"mafft\")\n \
+ {\n my $base=cwd();\n my $c;\n \n #compile co\
+re\n mkpath (\"./mafft/bin\");\n mkpath (\"./mafft\
+/lib\");\n chdir \"$base/core\";\n `make clean $SI\
+LENT`;\n &flush_command (\"make $arguments\");\n &\
+flush_command (\"make install LIBDIR=../mafft/lib \
+BINDIR=../mafft/bin\");\n \n #compile extension\n \
+chdir \"$base/extensions\";\n `make clean $SILENT`\
+;\n &flush_command (\"make $arguments\");\n &flush\
+_command (\"make install LIBDIR=../mafft/lib BINDI\
+R=../mafft/bin\");\n \n #put everything in mafft a\
+nd copy the compiled stuff in bin\n chdir \"$base\\
+";\n if ($ROOT_INSTALL)\n {\n &root_run (\"Y\
+ou Must be Root to Install MAFFT\\n\", \"mkdir /us\
+r/local/mafft/;$CP mafft/lib/* /usr/local/mafft;$C\
+P mafft/lib/mafft* /usr/local/bin ;$CP mafft/bin/m\
+afft /usr/local/bin/; \");\n }\n else\n {\n \
+ `$CP mafft/lib/* $BIN`;\n `$CP mafft/bin/ma\
+fft $BIN`;\n }\n `tar -cvf mafft.tar mafft`;\n \
+`gzip mafft.tar`;\n `mv mafft.tar.gz $BIN`;\n \n r\
+epo_store(\"mafft/bin/mafft\", \"mafft/lib/\", \"$\
+BIN/mafft.tar.gz\");\n }\n \n #\n \
+# DIALIGN-TX module\n #\n elsif ( $pg eq \"d\
+ialign-tx\" )\n {\n my $f;\n my $base=cwd();\\
+n\n chdir \"./source\";\n if ($OS eq \"macosx\"){&\
+flush_command (\"cp makefile.MAC_OS makefile\");}\\
+n\n &flush_command (\" make CPPFLAGS='-O3 -funroll\
+-loops' all\");\n \n chdir \"..\";\n &check_cp (\"\
+./source/$pg\", \"$BIN\");\n repo_store(\"./source\
+/$pg\");\n }\n \n #\n # DIALIGN-T \
+module \n # (is the same as dialign-tx, but it \
+is mantained for backward name compatibility with \
+tcoffee)\n #\n elsif ( $pg eq \"dialign-t\" \
+)\n {\n my $f;\n my $base=cwd();\n\n chdir \"\
+./source\";\n if ($OS eq \"macosx\"){&flush_comman\
+d (\"cp makefile.MAC_OS makefile\");}\n\n &flush_c\
+ommand (\" make CPPFLAGS='-O3 -funroll-loops' all\\
+");\n \n chdir \"..\";\n &check_cp (\"./source/dia\
+lign-tx\", \"$BIN/dialign-t\");\n repo_store(\"$BI\
+N/dialign-t\"); \n } \n \n #\n \
+ # POA module\n #\n elsif ($pg eq \"poa\")\\
+n {\n &flush_command (\"make $arguments poa\"\
+);\n &check_cp (\"$pg\", \"$BIN\");\n repo_store(\\
+"$pg\");\n }\n \n \n #\n # PROB\
+CONS module\n #\n elsif ( $pg eq \"probcons\\
+")\n {\n &add_C_libraries(\"./ProbabilisticMo\
+del.h\", \"list\", \"cstring\");\n \n `rm *.exe $S\
+ILENT`;\n &flush_command (\"make $arguments probco\
+ns\");\n &check_cp(\"$pg\", \"$BIN/$pg\");\n repo_\
+store(\"$pg\");\n }\n \n #\n # PRO\
+BCONS RNA module\n #\n elsif ( $pg eq \"prob\
+consRNA\")\n {\n &add_C_libraries(\"./Probabi\
+listicModel.h\", \"list\", \"cstring\");\n &add_C_\
+libraries(\"./Main.cc\", \"iomanip\", \"cstring\",\
+\"climits\");\n `rm *.exe $SILENT`;\n &flush_comma\
+nd (\"make $arguments probcons\");\n &check_cp(\"p\
+robcons\", \"$BIN/$pg\");\n repo_store(\"$BIN/$pg\\
+");\n }\n\n #\n # MUSCLE module\n #\n elsi\
+f ( $pg eq \"muscle\")\n { \n `rm *.o muscle\
+ muscle.exe $SILENT`;\n if ($OS eq \"macosx\" || $\
+OS eq \"linux\")\n {\n &replace_line_in_file\
+ (\"./Makefile\", \"LDLIBS = -lm -static\", \"LDL\
+IBS = -lm\");\n }\n elsif ($OS eq \"windows\")\n\
+ {\n &replace_line_in_file (\"./intmath.cpp\\
+", \"double log2e\", \"double cedric_log\");\
+\n &replace_line_in_file (\"./intmath.cpp\", \
+\"double log2\", \"double log_notuse\");\n \
+ &replace_line_in_file (\"./intmath.cpp\", \"do\
+uble cedric_log\", \"double log2e\");\n }\n &flu\
+sh_command (\"make $arguments all\");\n &check_cp(\
+\"$pg\", \"$BIN\");\n repo_store(\"$pg\"); \n \
+ }\n \n #\n # MUS4 module\n #\n \
+ elsif ( $pg eq \"mus4\")\n {\n `rm *.o mu\
+scle muscle.exe $SILENT`;\n &flush_command (\"./mk\
+\");\n &check_cp(\"$pg\", \"$BIN\");\n repo_store(\
+\"$pg\"); \n }\n \n #\n # PCMA mod\
+ule\n #\n elsif ( $pg eq \"pcma\")\n {\\
+n if ($OS eq \"macosx\")\n {\n &replace_line\
+_in_file (\"./alcomp2.c\", \"malloc.h\", \"\");\n\
+ }\n &flush_command (\"make $arguments pcma\");\\
+n &check_cp(\"$pg\", \"$BIN\");\n repo_store(\"$pg\
+\"); \n }\n \n #\n # KALIGN module\
+\n #\n elsif ($pg eq \"kalign\")\n {\n \
+&flush_command (\"./configure\");\n &flush_command\
+(\"make $arguments\");\n &check_cp (\"$pg\",$BIN);\
+\n repo_store(\"$pg\"); \n }\n \n #\n\
+ # AMAP module\n #\n elsif ( $pg eq \"ama\
+p\")\n {\n &add_C_libraries(\"./Amap.cc\", \"\
+iomanip\", \"cstring\",\"climits\"); \n `make clea\
+n $SILENT`;\n &flush_command (\"make $arguments al\
+l\");\n &check_cp (\"$pg\", $BIN);\n repo_store(\"\
+$pg\"); \n }\n \n #\n # PRODA modu\
+le\n #\n elsif ( $pg eq \"proda\")\n {\\
+n &add_C_libraries(\"AlignedFragment.h\", \"vector\
+\", \"iostream\", \"cstring\",\"cstdlib\");\n &add\
+_C_libraries(\"Main.cc\", \"vector\", \"climits\")\
+; \n &add_C_libraries(\"Sequence.cc\", \"stdlib.h\\
+", \"cstdio\"); \n &flush_command (\"make $argumen\
+ts all\");\n &check_cp (\"$pg\", $BIN);\n repo_sto\
+re(\"$pg\"); \n }\n \n #\n # PRANK\
+ module\n #\n elsif ( $pg eq \"prank\")\n \
+ {\n &flush_command (\"make $arguments all\");\n\
+ &check_cp (\"$pg\", $BIN);\n repo_store(\"$pg\");\
+ \n }\n \n #\n # !!!! MUSTANG modu\
+le\n #\n elsif ( $pg eq \"mustang\")\n \
+ {\n &flush_command (\"rm ./bin/*\");\n &flush_com\
+mand (\"make $arguments all\");\n\n if ( $OS=~/win\
+dows/){&flush_command(\"cp ./bin/* $BIN/mustang.ex\
+e\");}\n else {&flush_command(\"cp ./bin/* $BIN/mu\
+stang\");}\n \n repo_store(\"$BIN/mustang\");\n \
+ }\n\n #\n # RNAplfold module\n #\n elsif ( $\
+pg eq \"RNAplfold\")\n {\n &flush_command(\".\
+/configure\");\n &flush_command (\"make $arguments\
+ all\");\n &check_cp(\"./Progs/RNAplfold\", \"$BIN\
+\");\n &check_cp(\"./Progs/RNAalifold\", \"$BIN\")\
+;\n &check_cp(\"./Progs/RNAfold\", \"$BIN\");\n \n\
+ repo_store(\"./Progs/RNAplfold\", \"./Progs/RNAal\
+ifold\", \"./Progs/RNAfold\");\n }\n \n \
+ #\n # !!! RETREE module\n #\n elsif ( \
+$pg eq \"retree\")\n {\n chdir \"src\";\n &fl\
+ush_command (\"make $arguments all\");\n &flush_co\
+mmand (\"make put\");\n system \"cp ../exe/* $BIN\\
+";\n \n repo_store(\"retree\", \"../exe\");\n \
+ }\n \n chdir $CDIR;\n return &pg_is_install\
+ed ($pg, $BIN);\n }\n\nsub install_t_coffee\n {\\
+n my ($pg)=(@_);\n my ($report,$cflags, $arg\
+uments, $language, $compiler) ;\n #1-Install T-\
+Coffee\n chdir \"t_coffee_source\";\n &flush\
+_command (\"make clean\");\n print \"\\n-------\
+ Compiling T-Coffee\\n\";\n $language=$PG{$pg} \
+{language2};\n $arguments=$PG{$language}{argume\
+nts};\n if (!($arguments =~/CFLAGS/)){$argument\
+s .= \" CFLAGS=-O2 \";}\n\n if ( $CC ne \"\"){&\
+flush_command (\"make -i $arguments t_coffee\");}\\
+n &check_cp ($pg, $BIN);\n \n chdir $CDIR\
+;\n return &pg_is_installed ($pg, $BIN);\n }\n\
+sub install_TMalign\n {\n my ($pg)=(@_);\n \
+my $report;\n chdir \"t_coffee_source\";\n p\
+rint \"\\n------- Compiling TMalign\\n\";\n `rm\
+ TMalign TMalign.exe $SILENT`;\n if ( $FC ne \"\
+\"){&flush_command (\"make -i $PG{Fortran}{argumen\
+ts} TMalign\");}\n &check_cp ($pg, $BIN);\n \
+repo_store($pg);\n\n if ( !-e \"$BIN/$pg\" && p\
+g_has_binary_distrib ($pg))\n {\n print \"!!!\
+!!!! Compilation of $pg impossible. Will try to in\
+stall from binary\\n\";\n return &install_binary_p\
+ackage ($pg);\n }\n chdir $CDIR;\n retu\
+rn &pg_is_installed ($pg, $BIN);\n }\n\nsub pg_ha\
+s_binary_distrib\n {\n my ($pg)=(@_);\n if \
+($PG{$pg}{windows}){return 1;}\n elsif ($PG{$pg\
+}{osx}){return 1;}\n elsif ($PG{$pg}{linux}){re\
+turn 1;}\n return 0;\n }\nsub install_binary_p\
+ackage\n {\n my ($pg)=(@_);\n my ($base,$re\
+port,$name, $download, $arguments, $language, $dir\
+);\n my $isdir;\n &input_os();\n \n if\
+ (!&supported_os($OS)){return 0;}\n if ( $PG{$p\
+g}{binary}){$name=$PG{$pg}{binary};}\n else \n \
+ {\n $name=$pg;\n if ( $OS eq \"windows\"){$na\
+me.=\".exe\";}\n }\n \n $download=\"$WE\
+B_BASE/Packages/Binaries/$OS/$name\";\n \n $\
+base=cwd();\n chdir $TMP;\n \n if (!-e $n\
+ame)\n {\n `rm x $SILENT`;\n if ( url2file(\"\
+$download\",\"x\")==$EXIT_SUCCESS)\n {\n `mv\
+ x $name`;\n }\n }\n \n if (!-e $name\
+)\n {\n print \"!!!!!!! $PG{$pg}{dname}: Down\
+load of $pg binary failed\\n\";\n print \"!!!!!!! \
+$PG{$pg}{dname}: Check Address: $download\\n\";\n \
+return 0;\n }\n print \"\\n------- Install\
+ing $pg\\n\";\n \n if ($name =~/tar\\.gz/)\n\
+ {\n `gunzip $name`;\n `tar -xvf $pg.tar`;\n\
+ chdir $pg;\n if ( $pg eq \"mafft\")\n {\n i\
+f ($ROOT_INSTALL)\n {\n &root_run (\"You Mu\
+st be Roor to Install MAFFT\\n\", \"$CP mafft/bin/\
+* /usr/local/mafft;mkdir /usr/local/mafft/; $CP ma\
+fft/lib/* /usr/local/bin/\");\n }\n else\
+\n {\n `$CP $TMP/$pg/bin/* $BIN $SILENT`;\n\
+ `$CP $TMP/$pg/lib/* $BIN $SILENT`;\n }\n \
+ }\n else\n {\n if (-e \"$TMP/$pg/data\"){`$\
+CP $TMP/$pg/data/* $TCM $SILENT`;}\n if (!($pg\
+=~/\\*/)){`rm -rf $pg`;}\n }\n }\n else\\
+n {\n &check_cp (\"$pg\", \"$BIN\");\n `chmod\
+ u+x $BIN/$pg`; \n unlink ($pg);\n }\n chd\
+ir $base;\n $PG{$pg}{from_binary}=1;\n retur\
+n &pg_is_installed ($pg, $BIN);\n }\n\nsub add_di\
+r \n {\n my $dir=@_[0];\n \n if (!-e $di\
+r && !-d $dir)\n {\n my @l;\n umask (0000);\n\
+ @l=mkpath ($dir,{mode => 0777});\n \n }\n \
+ else\n {\n return 0;\n }\n }\nsub chec\
+k_rm \n {\n my ($file)=(@_);\n \n if ( -\
+e $file)\n {\n return unlink($file);\n }\
+\n return 0;\n }\nsub check_cp\n {\n my ($\
+from, $to)=(@_);\n if ( !-e $from && -e \"$from\
+\\.exe\"){$from=\"$from\\.exe\";}\n if ( !-e $f\
+rom){return 0;}\n \n `$CP $from $to`;\n \
+ return 1;\n }\n\nsub repo_store \n{\n # chec\
+k that all required data are available\n if( $RE\
+PO_ROOT eq \"\" ) { return; }\n\n\n # extract t\
+he package name from the specified path\n my $p\
+g =`basename $_[0]`;\n chomp($pg);\n \n my $\
+VER = $PG{$pg}{version};\n my $CACHE = \"$REPO_\
+ROOT/$pg/$VER/$OSNAME-$OSARCH\"; \n \n print\
+ \"-------- Storing package: \\\"$pg\\\" to path: \
+$CACHE\\n\";\n \n # clean the cache path if \
+exists and create it again\n `rm -rf $CACHE`;\n\
+ `mkdir -p $CACHE`;\n \n for my $path (@_) \
+{\n\n # check if it is a single file \n if( \
+-f $path ) {\n `cp $path $CACHE`;\n }\n # .\
+. or a directory, in this case copy all the conten\
+t \n elsif( -d $path ) {\n opendir(IMD, $path);\
+\n my @thefiles= readdir(IMD);\n closedir(IMD)\
+;\n \n for my $_file (@thefiles) {\n if( $_\
+file ne \".\" && $_file ne \"..\") {\n `cp \
+$path/$_file $CACHE`;\n }\n }\n } \n } \n\
+ \n \n} \n\nsub repo_load \n{\n my ($pg)=(\
+@_);\n\n # check that all required data are ava\
+ilable\n if( $REPO_ROOT eq \"\" ) { return 0; }\
+\n\n my $VER = $PG{$pg}{version};\n my $CACH\
+E = \"$REPO_ROOT/$pg/$VER/$OSNAME-$OSARCH\"; \n \
+ if( !-e \"$CACHE/$pg\" ) {\n print \"-------\
+- Module \\\"$pg\\\" NOT found on repository cache\
+.\\n\";\n return 0;\n }\n \n print \"\
+-------- Module \\\"$pg\\\" found on repository ca\
+che. Using copy on path: $CACHE\\n\";\n `cp $CA\
+CHE/* $BIN`;\n return 1;\n}\n\nsub check_file_l\
+ist_exists \n {\n my ($base, @flist)=(@_);\n \
+ my $f;\n\n foreach $f (@flist)\n {\n if \
+( !-e \"$base/$f\"){return 0;}\n }\n retur\
+n 1;\n }\nsub ls\n {\n my $f=@_[0];\n my @\
+fl;\n chomp(@fl=`ls -1 $f`);\n return @fl;\n\
+ }\nsub flush_command\n {\n my $command=@_[0]\
+;\n my $F=new FileHandle;\n open ($F, \"$com\
+mand|\");\n while (<$F>){print \" --- $_\";}\
+\n close ($F);\n } \n\nsub input_installati\
+on_directory\n {\n my $dir=@_[0];\n my $new\
+;\n \n print \"------- The current installat\
+ion directory is: [$dir]\\n\";\n print \"??????\
+? Return to keep the default or new value:\";\n \
+\n if ($NO_QUESTION==0)\n {\n chomp ($new=\
+<stdin>);\n while ( $new ne \"\" && !input_yes (\"\
+You have entered $new. Is this correct? ([y]/n):\"\
+))\n {\n print \"???????New installation dir\
+ectory:\";\n chomp ($new=<stdin>);\n }\n $di\
+r=($new eq \"\")?$dir:$new;\n $dir=~s/\\/$//;\n \
+ }\n \n if ( -d $dir){return $dir;}\n e\
+lsif (&root_run (\"You must be root to create $dir\
+\",\"mkdir $dir\")==$EXIT_SUCCESS){return $dir;}\n\
+ else\n {\n print \"!!!!!!! $dir could not\
+ be created\\n\";\n if ( $NO_QUESTION)\n {\n \
+ return \"\";\n }\n elsif ( &input_yes (\"??????\
+? Do you want to provide a new directory([y]/n)?:\\
+"))\n {\n return input_installation_director\
+y ($dir);\n }\n else\n {\n return \"\";\n \
+ }\n }\n \n }\nsub input_yes\n {\n m\
+y $question =@_[0];\n my $answer;\n\n if ($N\
+O_QUESTION==1){return 1;}\n \n if ($question\
+ eq \"\"){$question=\"??????? Do you wish to proce\
+ed ([y]/n)?:\";}\n print $question;\n chomp(\
+$answer=lc(<STDIN>));\n if (($answer=~/^y/) || \
+$answer eq \"\"){return 1;}\n elsif ( ($answer=\
+~/^n/)){return 0;}\n else\n {\n return inp\
+ut_yes($question);\n }\n }\nsub root_run\n \
+{\n my ($txt, $cmd)=(@_);\n \n if ( syste\
+m ($cmd)==$EXIT_SUCCESS){return $EXIT_SUCCESS;}\n \
+ else \n {\n print \"------- $txt\\n\";\n i\
+f ( $ROOT eq \"sudo\"){return system (\"sudo $cmd\\
+");}\n else {return system (\"su root -c \\\"$cmd\\
+\\"\");}\n }\n }\nsub get_root\n {\n if \
+(&pg_is_installed (\"sudo\")){return \"sudo\";}\n \
+ else {return \"su\";}\n }\n\nsub get_os\n {\n\
+ my $raw_os=`uname`;\n my $os;\n\n $raw_o\
+s=lc ($raw_os);\n \n if ($raw_os =~/cygwin/)\
+{$os=\"windows\";}\n elsif ($raw_os =~/linux/){\
+$os=\"linux\";}\n elsif ($raw_os =~/osx/){$os=\\
+"macosx\";}\n elsif ($raw_os =~/darwin/){$os=\"\
+macosx\";}\n else\n {\n $os=$raw_os;\n \
+ }\n return $os;\n }\nsub input_os\n {\n \
+my $answer;\n if ($OS) {return $OS;}\n \n \
+ print \"??????? which os do you use: [w]indows, [\
+l]inux, [m]acosx:?\";\n $answer=lc(<STDIN>);\n\\
+n if (($answer=~/^m/)){$OS=\"macosx\";}\n el\
+sif ( ($answer=~/^w/)){$OS=\"windows\";}\n elsi\
+f ( ($answer=~/^linux/)){$OS=\"linux\";}\n \n \
+ else\n {\n return &input_os();\n }\n \
+ return $OS;\n }\n\nsub supported_os\n {\n m\
+y ($os)=(@_[0]);\n return $SUPPORTED_OS{$os};\n\
+ }\n \n \n\n\nsub update_tclinkdb \n {\n \
+ my $file =@_[0];\n my $name;\n my $F=new F\
+ileHandle;\n my ($download, $address, $name, $l\
+, $db);\n \n if ( $file eq \"update\"){$file\
+=$TCLINKDB_ADDRESS;}\n \n if ( $file =~/http\
+:\\/\\// || $file =~/ftp:\\/\\//)\n {\n ($add\
+ress, $name)=($download=~/(.*)\\/([^\\/]+)$/);\n `\
+rm x $SILENT`;\n if (&url2file ($file,\"x\")==$EXI\
+T_SUCCESS)\n {\n print \"------- Susscessful\
+ upload of $name\";\n `mv x $name`;\n $fil\
+e=$name;\n }\n }\n open ($F, \"$file\");\
+\n while (<$F>)\n {\n my $l=$_;\n if (($l \
+=~/^\\/\\//) || ($db=~/^#/)){;}\n elsif ( !($l =~/\
+\\w/)){;}\n else\n {\n my @v=split (/\\s+/, \
+$l);\n if ( $l=~/^MODE/)\n {\n $MODE{$v\
+[1]}{$v[2]}=$v[3];\n }\n elsif ($l=~/^PG\
+/)\n {\n $PG{$v[1]}{$v[2]}=$v[3];\n }\
+\n }\n }\n close ($F);\n &post_proces\
+s_PG();\n return;\n }\n\n\n\nsub initialize_PG\
+\n {\n\n$PG{\"t_coffee\"}{\"4_TCOFFEE\"}=\"TCOFFE\
+E\";\n$PG{\"t_coffee\"}{\"type\"}=\"sequence_multi\
+ple_aligner\";\n$PG{\"t_coffee\"}{\"ADDRESS\"}=\"h\
+ttp://www.tcoffee.org\";\n$PG{\"t_coffee\"}{\"lang\
+uage\"}=\"C\";\n$PG{\"t_coffee\"}{\"language2\"}=\\
+"C\";\n$PG{\"t_coffee\"}{\"source\"}=\"http://www.\
+tcoffee.org/Packages/T-COFFEE_distribution.tar.gz\\
+";\n$PG{\"t_coffee\"}{\"update_action\"}=\"always\\
+";\n$PG{\"t_coffee\"}{\"mode\"}=\"tcoffee,mcoffee,\
+rcoffee,expresso,3dcoffee\";\n$PG{\"clustalw2\"}{\\
+"4_TCOFFEE\"}=\"CLUSTALW2\";\n$PG{\"clustalw2\"}{\\
+"type\"}=\"sequence_multiple_aligner\";\n$PG{\"clu\
+stalw2\"}{\"ADDRESS\"}=\"http://www.clustal.org\";\
+\n$PG{\"clustalw2\"}{\"language\"}=\"C++\";\n$PG{\\
+"clustalw2\"}{\"language2\"}=\"CXX\";\n$PG{\"clust\
+alw2\"}{\"source\"}=\"http://www.clustal.org/downl\
+oad/2.0.10/clustalw-2.0.10-src.tar.gz\";\n$PG{\"cl\
+ustalw2\"}{\"mode\"}=\"mcoffee,rcoffee\";\n$PG{\"c\
+lustalw2\"}{\"version\"}=\"2.0.10\";\n$PG{\"clusta\
+lw\"}{\"4_TCOFFEE\"}=\"CLUSTALW\";\n$PG{\"clustalw\
+\"}{\"type\"}=\"sequence_multiple_aligner\";\n$PG{\
+\"clustalw\"}{\"ADDRESS\"}=\"http://www.clustal.or\
+g\";\n$PG{\"clustalw\"}{\"language\"}=\"C\";\n$PG{\
+\"clustalw\"}{\"language2\"}=\"C\";\n$PG{\"clustal\
+w\"}{\"source\"}=\"http://www.clustal.org/download\
+/1.X/ftp-igbmc.u-strasbg.fr/pub/ClustalW/clustalw1\
+.82.UNIX.tar.gz\";\n$PG{\"clustalw\"}{\"mode\"}=\"\
+mcoffee,rcoffee\";\n$PG{\"clustalw\"}{\"version\"}\
+=\"1.82\";\n$PG{\"dialign-t\"}{\"4_TCOFFEE\"}=\"DI\
+ALIGNT\";\n$PG{\"dialign-t\"}{\"type\"}=\"sequence\
+_multiple_aligner\";\n$PG{\"dialign-t\"}{\"ADDRESS\
+\"}=\"http://dialign-tx.gobics.de/\";\n$PG{\"diali\
+gn-t\"}{\"DIR\"}=\"/usr/share/dialign-tx/\";\n$PG{\
+\"dialign-t\"}{\"language\"}=\"C\";\n$PG{\"dialign\
+-t\"}{\"language2\"}=\"C\";\n$PG{\"dialign-t\"}{\"\
+source\"}=\"http://dialign-tx.gobics.de/DIALIGN-TX\
+_1.0.2.tar.gz\";\n$PG{\"dialign-t\"}{\"mode\"}=\"m\
+coffee\";\n$PG{\"dialign-t\"}{\"binary\"}=\"dialig\
+n-t\";\n$PG{\"dialign-t\"}{\"version\"}=\"1.0.2\";\
+\n$PG{\"dialign-tx\"}{\"4_TCOFFEE\"}=\"DIALIGNTX\"\
+;\n$PG{\"dialign-tx\"}{\"type\"}=\"sequence_multip\
+le_aligner\";\n$PG{\"dialign-tx\"}{\"ADDRESS\"}=\"\
+http://dialign-tx.gobics.de/\";\n$PG{\"dialign-tx\\
+"}{\"DIR\"}=\"/usr/share/dialign-tx/\";\n$PG{\"dia\
+lign-tx\"}{\"language\"}=\"C\";\n$PG{\"dialign-tx\\
+"}{\"language2\"}=\"C\";\n$PG{\"dialign-tx\"}{\"so\
+urce\"}=\"http://dialign-tx.gobics.de/DIALIGN-TX_1\
+.0.2.tar.gz\";\n$PG{\"dialign-tx\"}{\"mode\"}=\"mc\
+offee\";\n$PG{\"dialign-tx\"}{\"binary\"}=\"dialig\
+n-tx\";\n$PG{\"dialign-tx\"}{\"version\"}=\"1.0.2\\
+";\n$PG{\"poa\"}{\"4_TCOFFEE\"}=\"POA\";\n$PG{\"po\
+a\"}{\"type\"}=\"sequence_multiple_aligner\";\n$PG\
+{\"poa\"}{\"ADDRESS\"}=\"http://www.bioinformatics\
+.ucla.edu/poa/\";\n$PG{\"poa\"}{\"language\"}=\"C\\
+";\n$PG{\"poa\"}{\"language2\"}=\"C\";\n$PG{\"poa\\
+"}{\"source\"}=\"http://downloads.sourceforge.net/\
+poamsa/poaV2.tar.gz\";\n$PG{\"poa\"}{\"DIR\"}=\"/u\
+sr/share/\";\n$PG{\"poa\"}{\"FILE1\"}=\"blosum80.m\
+at\";\n$PG{\"poa\"}{\"mode\"}=\"mcoffee\";\n$PG{\"\
+poa\"}{\"binary\"}=\"poa\";\n$PG{\"poa\"}{\"versio\
+n\"}=\"2.0\";\n$PG{\"probcons\"}{\"4_TCOFFEE\"}=\"\
+PROBCONS\";\n$PG{\"probcons\"}{\"type\"}=\"sequenc\
+e_multiple_aligner\";\n$PG{\"probcons\"}{\"ADDRESS\
+\"}=\"http://probcons.stanford.edu/\";\n$PG{\"prob\
+cons\"}{\"language2\"}=\"CXX\";\n$PG{\"probcons\"}\
+{\"language\"}=\"C++\";\n$PG{\"probcons\"}{\"sourc\
+e\"}=\"http://probcons.stanford.edu/probcons_v1_12\
+.tar.gz\";\n$PG{\"probcons\"}{\"mode\"}=\"mcoffee\\
+";\n$PG{\"probcons\"}{\"binary\"}=\"probcons\";\n$\
+PG{\"probcons\"}{\"version\"}=\"1.12\";\n$PG{\"maf\
+ft\"}{\"4_TCOFFEE\"}=\"MAFFT\";\n$PG{\"mafft\"}{\"\
+type\"}=\"sequence_multiple_aligner\";\n$PG{\"maff\
+t\"}{\"ADDRESS\"}=\"http://align.bmr.kyushu-u.ac.j\
+p/mafft/online/server/\";\n$PG{\"mafft\"}{\"langua\
+ge\"}=\"C\";\n$PG{\"mafft\"}{\"language\"}=\"C\";\\
+n$PG{\"mafft\"}{\"source\"}=\"http://align.bmr.kyu\
+shu-u.ac.jp/mafft/software/mafft-6.603-with-extens\
+ions-src.tgz\";\n$PG{\"mafft\"}{\"windows\"}=\"htt\
+p://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-\
+6.603-mingw.tar\";\n$PG{\"mafft\"}{\"mode\"}=\"mco\
+ffee,rcoffee\";\n$PG{\"mafft\"}{\"binary\"}=\"maff\
+t.tar.gz\";\n$PG{\"mafft\"}{\"version\"}=\"6.603\"\
+;\n$PG{\"muscle\"}{\"4_TCOFFEE\"}=\"MUSCLE\";\n$PG\
+{\"muscle\"}{\"type\"}=\"sequence_multiple_aligner\
+\";\n$PG{\"muscle\"}{\"ADDRESS\"}=\"http://www.dri\
+ve5.com/muscle/\";\n$PG{\"muscle\"}{\"language\"}=\
+\"C++\";\n$PG{\"muscle\"}{\"language2\"}=\"GPP\";\\
+n$PG{\"muscle\"}{\"source\"}=\"http://www.drive5.c\
+om/muscle/downloads3.7/muscle3.7_src.tar.gz\";\n$P\
+G{\"muscle\"}{\"windows\"}=\"http://www.drive5.com\
+/muscle/downloads3.7/muscle3.7_win32.zip\";\n$PG{\\
+"muscle\"}{\"linux\"}=\"http://www.drive5.com/musc\
+le/downloads3.7/muscle3.7_linux_ia32.tar.gz\";\n$P\
+G{\"muscle\"}{\"mode\"}=\"mcoffee,rcoffee\";\n$PG{\
+\"muscle\"}{\"version\"}=\"3.7\";\n$PG{\"mus4\"}{\\
+"4_TCOFFEE\"}=\"MUS4\";\n$PG{\"mus4\"}{\"type\"}=\\
+"sequence_multiple_aligner\";\n$PG{\"mus4\"}{\"ADD\
+RESS\"}=\"http://www.drive5.com/muscle/\";\n$PG{\"\
+mus4\"}{\"language\"}=\"C++\";\n$PG{\"mus4\"}{\"la\
+nguage2\"}=\"GPP\";\n$PG{\"mus4\"}{\"source\"}=\"h\
+ttp://www.drive5.com/muscle/muscle4.0_src.tar.gz\"\
+;\n$PG{\"mus4\"}{\"mode\"}=\"mcoffee,rcoffee\";\n$\
+PG{\"mus4\"}{\"version\"}=\"4.0\";\n$PG{\"pcma\"}{\
+\"4_TCOFFEE\"}=\"PCMA\";\n$PG{\"pcma\"}{\"type\"}=\
+\"sequence_multiple_aligner\";\n$PG{\"pcma\"}{\"AD\
+DRESS\"}=\"ftp://iole.swmed.edu/pub/PCMA/\";\n$PG{\
+\"pcma\"}{\"language\"}=\"C\";\n$PG{\"pcma\"}{\"la\
+nguage2\"}=\"C\";\n$PG{\"pcma\"}{\"source\"}=\"ftp\
+://iole.swmed.edu/pub/PCMA/pcma.tar.gz\";\n$PG{\"p\
+cma\"}{\"mode\"}=\"mcoffee\";\n$PG{\"pcma\"}{\"ver\
+sion\"}=\"1.0\";\n$PG{\"kalign\"}{\"4_TCOFFEE\"}=\\
+"KALIGN\";\n$PG{\"kalign\"}{\"type\"}=\"sequence_m\
+ultiple_aligner\";\n$PG{\"kalign\"}{\"ADDRESS\"}=\\
+"http://msa.cgb.ki.se\";\n$PG{\"kalign\"}{\"langua\
+ge\"}=\"C\";\n$PG{\"kalign\"}{\"language2\"}=\"C\"\
+;\n$PG{\"kalign\"}{\"source\"}=\"http://msa.cgb.ki\
+.se/downloads/kalign/current.tar.gz\";\n$PG{\"kali\
+gn\"}{\"mode\"}=\"mcoffee\";\n$PG{\"kalign\"}{\"ve\
+rsion\"}=\"1.0\";\n$PG{\"amap\"}{\"4_TCOFFEE\"}=\"\
+AMAP\";\n$PG{\"amap\"}{\"type\"}=\"sequence_multip\
+le_aligner\";\n$PG{\"amap\"}{\"ADDRESS\"}=\"http:/\
+/bio.math.berkeley.edu/amap/\";\n$PG{\"amap\"}{\"l\
+anguage\"}=\"C++\";\n$PG{\"amap\"}{\"language2\"}=\
+\"CXX\";\n$PG{\"amap\"}{\"source\"}=\"http://amap-\
+align.googlecode.com/files/amap.2.0.tar.gz\";\n$PG\
+{\"amap\"}{\"mode\"}=\"mcoffee\";\n$PG{\"amap\"}{\\
+"version\"}=\"2.0\";\n$PG{\"proda\"}{\"4_TCOFFEE\"\
+}=\"PRODA\";\n$PG{\"proda\"}{\"type\"}=\"sequence_\
+multiple_aligner\";\n$PG{\"proda\"}{\"ADDRESS\"}=\\
+"http://proda.stanford.edu\";\n$PG{\"proda\"}{\"la\
+nguage\"}=\"C++\";\n$PG{\"proda\"}{\"language2\"}=\
+\"CXX\";\n$PG{\"proda\"}{\"source\"}=\"http://prod\
+a.stanford.edu/proda_1_0.tar.gz\";\n$PG{\"proda\"}\
+{\"mode\"}=\"mcoffee\";\n$PG{\"proda\"}{\"version\\
+"}=\"1.0\";\n$PG{\"fsa\"}{\"4_TCOFFEE\"}=\"FSA\";\\
+n$PG{\"fsa\"}{\"type\"}=\"sequence_multiple_aligne\
+r\";\n$PG{\"fsa\"}{\"ADDRESS\"}=\"http://fsa.sourc\
+eforge.net/\";\n$PG{\"fsa\"}{\"language\"}=\"C++\"\
+;\n$PG{\"fsa\"}{\"language2\"}=\"CXX\";\n$PG{\"fsa\
+\"}{\"source\"}=\"http://sourceforge.net/projects/\
+fsa/files/fsa-1.15.3.tar.gz/download/\";\n$PG{\"fs\
+a\"}{\"mode\"}=\"mcoffee\";\n$PG{\"fsa\"}{\"versio\
+n\"}=\"1.15.3\";\n$PG{\"prank\"}{\"4_TCOFFEE\"}=\"\
+PRANK\";\n$PG{\"prank\"}{\"type\"}=\"sequence_mult\
+iple_aligner\";\n$PG{\"prank\"}{\"ADDRESS\"}=\"htt\
+p://www.ebi.ac.uk/goldman-srv/prank/\";\n$PG{\"pra\
+nk\"}{\"language\"}=\"C++\";\n$PG{\"prank\"}{\"lan\
+guage2\"}=\"CXX\";\n$PG{\"prank\"}{\"source\"}=\"h\
+ttp://www.ebi.ac.uk/goldman-srv/prank/src/prank/pr\
+ank.src.100303.tgz\";\n$PG{\"prank\"}{\"mode\"}=\"\
+mcoffee\";\n$PG{\"prank\"}{\"version\"}=\"100303\"\
+;\n$PG{\"sap\"}{\"4_TCOFFEE\"}=\"SAP\";\n$PG{\"sap\
+\"}{\"type\"}=\"structure_pairwise_aligner\";\n$PG\
+{\"sap\"}{\"ADDRESS\"}=\"http://mathbio.nimr.mrc.a\
+c.uk/wiki/Software\";\n$PG{\"sap\"}{\"language\"}=\
+\"C\";\n$PG{\"sap\"}{\"language2\"}=\"C\";\n$PG{\"\
+sap\"}{\"source\"}=\"http://mathbio.nimr.mrc.ac.uk\
+/download/sap-1.1.1.tar.gz\";\n$PG{\"sap\"}{\"mode\
+\"}=\"expresso,3dcoffee\";\n$PG{\"sap\"}{\"version\
+\"}=\"1.1.1\";\n$PG{\"TMalign\"}{\"4_TCOFFEE\"}=\"\
+TMALIGN\";\n$PG{\"TMalign\"}{\"type\"}=\"structure\
+_pairwise_aligner\";\n$PG{\"TMalign\"}{\"ADDRESS\"\
+}=\"http://zhang.bioinformatics.ku.edu/TM-align/TM\
+align.f\";\n$PG{\"TMalign\"}{\"language\"}=\"Fortr\
+an\";\n$PG{\"TMalign\"}{\"language2\"}=\"Fortran\"\
+;\n$PG{\"TMalign\"}{\"source\"}=\"http://zhang.bio\
+informatics.ku.edu/TM-align/TMalign.f\";\n$PG{\"TM\
+align\"}{\"linux\"}=\"http://zhang.bioinformatics.\
+ku.edu/TM-align/TMalign_32.gz\";\n$PG{\"TMalign\"}\
+{\"mode\"}=\"expresso,3dcoffee\";\n$PG{\"TMalign\"\
+}{\"version\"}=\"1.0\";\n$PG{\"mustang\"}{\"4_TCOF\
+FEE\"}=\"MUSTANG\";\n$PG{\"mustang\"}{\"type\"}=\"\
+structure_pairwise_aligner\";\n$PG{\"mustang\"}{\"\
+ADDRESS\"}=\"http://www.cs.mu.oz.au/~arun/mustang\\
+";\n$PG{\"mustang\"}{\"language\"}=\"C++\";\n$PG{\\
+"mustang\"}{\"language2\"}=\"CXX\";\n$PG{\"mustang\
+\"}{\"source\"}=\"http://ww2.cs.mu.oz.au/~arun/mus\
+tang/mustang_v3.2.1.tgz\";\n$PG{\"mustang\"}{\"mod\
+e\"}=\"expresso,3dcoffee\";\n$PG{\"mustang\"}{\"ve\
+rsion\"}=\"3.2.1\";\n$PG{\"lsqman\"}{\"4_TCOFFEE\"\
+}=\"LSQMAN\";\n$PG{\"lsqman\"}{\"type\"}=\"structu\
+re_pairwise_aligner\";\n$PG{\"lsqman\"}{\"ADDRESS\\
+"}=\"empty\";\n$PG{\"lsqman\"}{\"language\"}=\"emp\
+ty\";\n$PG{\"lsqman\"}{\"language2\"}=\"empty\";\n\
+$PG{\"lsqman\"}{\"source\"}=\"empty\";\n$PG{\"lsqm\
+an\"}{\"update_action\"}=\"never\";\n$PG{\"lsqman\\
+"}{\"mode\"}=\"expresso,3dcoffee\";\n$PG{\"align_p\
+db\"}{\"4_TCOFFEE\"}=\"ALIGN_PDB\";\n$PG{\"align_p\
+db\"}{\"type\"}=\"structure_pairwise_aligner\";\n$\
+PG{\"align_pdb\"}{\"ADDRESS\"}=\"empty\";\n$PG{\"a\
+lign_pdb\"}{\"language\"}=\"empty\";\n$PG{\"align_\
+pdb\"}{\"language2\"}=\"empty\";\n$PG{\"align_pdb\\
+"}{\"source\"}=\"empty\";\n$PG{\"align_pdb\"}{\"up\
+date_action\"}=\"never\";\n$PG{\"align_pdb\"}{\"mo\
+de\"}=\"expresso,3dcoffee\";\n$PG{\"fugueali\"}{\"\
+4_TCOFFEE\"}=\"FUGUE\";\n$PG{\"fugueali\"}{\"type\\
+"}=\"structure_pairwise_aligner\";\n$PG{\"fugueali\
+\"}{\"ADDRESS\"}=\"http://www-cryst.bioc.cam.ac.uk\
+/fugue/download.html\";\n$PG{\"fugueali\"}{\"langu\
+age\"}=\"empty\";\n$PG{\"fugueali\"}{\"language2\"\
+}=\"empty\";\n$PG{\"fugueali\"}{\"source\"}=\"empt\
+y\";\n$PG{\"fugueali\"}{\"update_action\"}=\"never\
+\";\n$PG{\"fugueali\"}{\"mode\"}=\"expresso,3dcoff\
+ee\";\n$PG{\"dalilite.pl\"}{\"4_TCOFFEE\"}=\"DALIL\
+ITEc\";\n$PG{\"dalilite.pl\"}{\"type\"}=\"structur\
+e_pairwise_aligner\";\n$PG{\"dalilite.pl\"}{\"ADDR\
+ESS\"}=\"built_in\";\n$PG{\"dalilite.pl\"}{\"ADDRE\
+SS2\"}=\"http://www.ebi.ac.uk/Tools/webservices/se\
+rvices/dalilite\";\n$PG{\"dalilite.pl\"}{\"languag\
+e\"}=\"Perl\";\n$PG{\"dalilite.pl\"}{\"language2\"\
+}=\"Perl\";\n$PG{\"dalilite.pl\"}{\"source\"}=\"em\
+pty\";\n$PG{\"dalilite.pl\"}{\"update_action\"}=\"\
+never\";\n$PG{\"dalilite.pl\"}{\"mode\"}=\"express\
+o,3dcoffee\";\n$PG{\"probconsRNA\"}{\"4_TCOFFEE\"}\
+=\"PROBCONSRNA\";\n$PG{\"probconsRNA\"}{\"type\"}=\
+\"RNA_multiple_aligner\";\n$PG{\"probconsRNA\"}{\"\
+ADDRESS\"}=\"http://probcons.stanford.edu/\";\n$PG\
+{\"probconsRNA\"}{\"language\"}=\"C++\";\n$PG{\"pr\
+obconsRNA\"}{\"language2\"}=\"CXX\";\n$PG{\"probco\
+nsRNA\"}{\"source\"}=\"http://probcons.stanford.ed\
+u/probconsRNA.tar.gz\";\n$PG{\"probconsRNA\"}{\"mo\
+de\"}=\"mcoffee,rcoffee\";\n$PG{\"probconsRNA\"}{\\
+"version\"}=\"1.0\";\n$PG{\"sfold\"}{\"4_TCOFFEE\"\
+}=\"CONSAN\";\n$PG{\"sfold\"}{\"type\"}=\"RNA_pair\
+wise_aligner\";\n$PG{\"sfold\"}{\"ADDRESS\"}=\"htt\
+p://selab.janelia.org/software/consan/\";\n$PG{\"s\
+fold\"}{\"language\"}=\"empty\";\n$PG{\"sfold\"}{\\
+"language2\"}=\"empty\";\n$PG{\"sfold\"}{\"source\\
+"}=\"empty\";\n$PG{\"sfold\"}{\"update_action\"}=\\
+"never\";\n$PG{\"sfold\"}{\"mode\"}=\"rcoffee\";\n\
+$PG{\"RNAplfold\"}{\"4_TCOFFEE\"}=\"RNAPLFOLD\";\n\
+$PG{\"RNAplfold\"}{\"type\"}=\"RNA_secondarystruct\
+ure_predictor\";\n$PG{\"RNAplfold\"}{\"ADDRESS\"}=\
+\"http://www.tbi.univie.ac.at/~ivo/RNA/\";\n$PG{\"\
+RNAplfold\"}{\"language\"}=\"C\";\n$PG{\"RNAplfold\
+\"}{\"language2\"}=\"C\";\n$PG{\"RNAplfold\"}{\"so\
+urce\"}=\"http://www.tbi.univie.ac.at/~ivo/RNA/Vie\
+nnaRNA-1.7.2.tar.gz\";\n$PG{\"RNAplfold\"}{\"mode\\
+"}=\"rcoffee,\";\n$PG{\"RNAplfold\"}{\"version\"}=\
+\"1.7.2\";\n$PG{\"retree\"}{\"4_TCOFFEE\"}=\"PHYLI\
+P\";\n$PG{\"retree\"}{\"type\"}=\"RNA_secondarystr\
+ucture_predictor\";\n$PG{\"retree\"}{\"ADDRESS\"}=\
+\"http://evolution.gs.washington.edu/phylip/\";\n$\
+PG{\"retree\"}{\"language\"}=\"C\";\n$PG{\"retree\\
+"}{\"language2\"}=\"C\";\n$PG{\"retree\"}{\"source\
+\"}=\"http://evolution.gs.washington.edu/phylip/do\
+wnload/phylip-3.69.tar.gz\";\n$PG{\"retree\"}{\"mo\
+de\"}=\"trmsd,\";\n$PG{\"retree\"}{\"version\"}=\"\
+3.69\";\n$PG{\"hmmtop\"}{\"4_TCOFFEE\"}=\"HMMTOP\"\
+;\n$PG{\"hmmtop\"}{\"type\"}=\"protein_secondaryst\
+ructure_predictor\";\n$PG{\"hmmtop\"}{\"ADDRESS\"}\
+=\"www.enzim.hu/hmmtop/\";\n$PG{\"hmmtop\"}{\"lang\
+uage\"}=\"C\";\n$PG{\"hmmtop\"}{\"language2\"}=\"C\
+\";\n$PG{\"hmmtop\"}{\"source\"}=\"empty\";\n$PG{\\
+"hmmtop\"}{\"update_action\"}=\"never\";\n$PG{\"hm\
+mtop\"}{\"mode\"}=\"tcoffee\";\n$PG{\"gorIV\"}{\"4\
+_TCOFFEE\"}=\"GOR4\";\n$PG{\"gorIV\"}{\"type\"}=\"\
+protein_secondarystructure_predictor\";\n$PG{\"gor\
+IV\"}{\"ADDRESS\"}=\"http://mig.jouy.inra.fr/logic\
+iels/gorIV/\";\n$PG{\"gorIV\"}{\"language\"}=\"C\"\
+;\n$PG{\"gorIV\"}{\"language2\"}=\"C\";\n$PG{\"gor\
+IV\"}{\"source\"}=\"http://mig.jouy.inra.fr/logici\
+els/gorIV/GOR_IV.tar.gz\";\n$PG{\"gorIV\"}{\"updat\
+e_action\"}=\"never\";\n$PG{\"gorIV\"}{\"mode\"}=\\
+"tcoffee\";\n$PG{\"wublast.pl\"}{\"4_TCOFFEE\"}=\"\
+EBIWUBLASTc\";\n$PG{\"wublast.pl\"}{\"type\"}=\"pr\
+otein_homology_predictor\";\n$PG{\"wublast.pl\"}{\\
+"ADDRESS\"}=\"built_in\";\n$PG{\"wublast.pl\"}{\"A\
+DDRESS2\"}=\"http://www.ebi.ac.uk/Tools/webservice\
+s/services/wublast\";\n$PG{\"wublast.pl\"}{\"langu\
+age\"}=\"Perl\";\n$PG{\"wublast.pl\"}{\"language2\\
+"}=\"Perl\";\n$PG{\"wublast.pl\"}{\"source\"}=\"em\
+pty\";\n$PG{\"wublast.pl\"}{\"update_action\"}=\"n\
+ever\";\n$PG{\"wublast.pl\"}{\"mode\"}=\"psicoffee\
+,expresso,accurate\";\n$PG{\"blastpgp.pl\"}{\"4_TC\
+OFFEE\"}=\"EBIBLASTPGPc\";\n$PG{\"blastpgp.pl\"}{\\
+"type\"}=\"protein_homology_predictor\";\n$PG{\"bl\
+astpgp.pl\"}{\"ADDRESS\"}=\"built_in\";\n$PG{\"bla\
+stpgp.pl\"}{\"ADDRESS2\"}=\"http://www.ebi.ac.uk/T\
+ools/webservices/services/blastpgp\";\n$PG{\"blast\
+pgp.pl\"}{\"language\"}=\"Perl\";\n$PG{\"blastpgp.\
+pl\"}{\"language2\"}=\"Perl\";\n$PG{\"blastpgp.pl\\
+"}{\"source\"}=\"empty\";\n$PG{\"blastpgp.pl\"}{\"\
+update_action\"}=\"never\";\n$PG{\"blastpgp.pl\"}{\
+\"mode\"}=\"psicoffee,expresso,accurate\";\n$PG{\"\
+blastcl3\"}{\"4_TCOFFEE\"}=\"NCBIWEBBLAST\";\n$PG{\
+\"blastcl3\"}{\"type\"}=\"protein_homology_predict\
+or\";\n$PG{\"blastcl3\"}{\"ADDRESS\"}=\"ftp://ftp.\
+ncbi.nih.gov/blast/executables/LATEST\";\n$PG{\"bl\
+astcl3\"}{\"language\"}=\"C\";\n$PG{\"blastcl3\"}{\
+\"language2\"}=\"C\";\n$PG{\"blastcl3\"}{\"source\\
+"}=\"empty\";\n$PG{\"blastcl3\"}{\"update_action\"\
+}=\"never\";\n$PG{\"blastcl3\"}{\"mode\"}=\"psicof\
+fee,expresso,3dcoffee\";\n$PG{\"blastpgp\"}{\"4_TC\
+OFFEE\"}=\"NCBIBLAST\";\n$PG{\"blastpgp\"}{\"type\\
+"}=\"protein_homology_predictor\";\n$PG{\"blastpgp\
+\"}{\"ADDRESS\"}=\"ftp://ftp.ncbi.nih.gov/blast/ex\
+ecutables/LATEST\";\n$PG{\"blastpgp\"}{\"language\\
+"}=\"C\";\n$PG{\"blastpgp\"}{\"language2\"}=\"C\";\
+\n$PG{\"blastpgp\"}{\"source\"}=\"empty\";\n$PG{\"\
+blastpgp\"}{\"update_action\"}=\"never\";\n$PG{\"b\
+lastpgp\"}{\"mode\"}=\"psicoffee,expresso,3dcoffee\
+\";\n$PG{\"SOAP::Lite\"}{\"4_TCOFFEE\"}=\"SOAPLITE\
+\";\n$PG{\"SOAP::Lite\"}{\"type\"}=\"library\";\n$\
+PG{\"SOAP::Lite\"}{\"ADDRESS\"}=\"http://cpansearc\
+h.perl.org/src/MKUTTER/SOAP-Lite-0.710.08/Makefile\
+.PL\";\n$PG{\"SOAP::Lite\"}{\"language\"}=\"Perl\"\
+;\n$PG{\"SOAP::Lite\"}{\"language2\"}=\"Perl\";\n$\
+PG{\"SOAP::Lite\"}{\"source\"}=\"empty\";\n$PG{\"b\
+lastpgp\"}{\"update_action\"}=\"never\";\n$PG{\"SO\
+AP::Lite\"}{\"mode\"}=\"none\";\n$PG{\"XML::Simple\
+\"}{\"4_TCOFFEE\"}=\"XMLSIMPLE\";\n$PG{\"XML::Simp\
+le\"}{\"type\"}=\"library\";\n$PG{\"XML::Simple\"}\
+{\"ADDRESS\"}=\"http://search.cpan.org/~grantm/XML\
+-Simple-2.18/lib/XML/Simple.pm\";\n$PG{\"XML::Simp\
+le\"}{\"language\"}=\"Perl\";\n$PG{\"XML::Simple\"\
+}{\"language2\"}=\"Perl\";\n$PG{\"XML::Simple\"}{\\
+"source\"}=\"empty\";\n$PG{\"XML::Simple\"}{\"mode\
+\"}=\"psicoffee,expresso,accurate\";\n$MODE{\"tcof\
+fee\"}{\"name\"}=\"tcoffee\";\n$MODE{\"rcoffee\"}{\
+\"name\"}=\"rcoffee\";\n$MODE{\"3dcoffee\"}{\"name\
+\"}=\"3dcoffee\";\n$MODE{\"mcoffee\"}{\"name\"}=\"\
+mcoffee\";\n$MODE{\"expresso\"}{\"name\"}=\"expres\
+so\";\n$MODE{\"trmsd\"}{\"name\"}=\"trmsd\";\n$MOD\
+E{\"accurate\"}{\"name\"}=\"accurate\";\n$MODE{\"s\
+eq_reformat\"}{\"name\"}=\"seq_reformat\";\n\n\n$P\
+G{C}{compiler}=\"gcc\";\n$PG{C}{compiler_flag}=\"C\
+C\";\n$PG{C}{options}=\"\";\n$PG{C}{options_flag}=\
+\"CFLAGS\";\n$PG{C}{type}=\"compiler\";\n\n$PG{\"C\
+XX\"}{compiler}=\"g++\";\n$PG{\"CXX\"}{compiler_fl\
+ag}=\"CXX\";\n$PG{\"CXX\"}{options}=\"\";\n$PG{\"C\
+XX\"}{options_flag}=\"CXXFLAGS\";\n$PG{CXX}{type}=\
+\"compiler\";\n\n$PG{\"CPP\"}{compiler}=\"g++\";\n\
+$PG{\"CPP\"}{compiler_flag}=\"CPP\";\n$PG{\"CPP\"}\
+{options}=\"\";\n$PG{\"CPP\"}{options_flag}=\"CPPF\
+LAGS\";\n$PG{CPP}{type}=\"compiler\";\n\n$PG{\"GPP\
+\"}{compiler}=\"g++\";\n$PG{\"GPP\"}{compiler_flag\
+}=\"GPP\";\n$PG{\"GPP\"}{options}=\"\";\n$PG{\"GPP\
+\"}{options_flag}=\"CFLAGS\";\n$PG{GPP}{type}=\"co\
+mpiler\";\n\n$PG{Fortran}{compiler}=\"g77\";\n$PG{\
+Fortran}{compiler_flag}=\"FCC\";\n$PG{Fortran}{typ\
+e}=\"compiler\";\n\n$PG{Perl}{compiler}=\"CPAN\";\\
+n$PG{Perl}{type}=\"compiler\";\n\n$SUPPORTED_OS{ma\
+cox}=\"Macintosh\";\n$SUPPORTED_OS{linux}=\"Linux\\
+";\n$SUPPORTED_OS{windows}=\"Cygwin\";\n\n\n\n$MOD\
+E{t_coffee}{description}=\" for regular multiple s\
+equence alignments\";\n$MODE{rcoffee} {description\
+}=\" for RNA multiple sequence alignments\";\n\n$M\
+ODE{psicoffee} {description}=\" for Homology Exten\
+ded multiple sequence alignments\";\n$MODE{express\
+o}{description}=\" for very accurate structure bas\
+ed multiple sequence alignments\";\n$MODE{\"3dcoff\
+ee\"}{description}=\" for multiple structure align\
+ments\";\n$MODE{mcoffee} {description}=\" for comb\
+ining alternative multiple sequence alignment pack\
+ages\\n------- into a unique meta-package. The ins\
+taller will upload several MSA packages and compil\
+e them\\n\n\";\n\n\n&post_process_PG();\nreturn;\n\
+}\n\nsub post_process_PG\n {\n my $p;\n \n \
+ %PG=&name2dname (%PG);\n %MODE=&name2dname(%\
+MODE);\n foreach $p (keys(%PG)){if ( $PG{$p}{ty\
+pe} eq \"compiler\"){$PG{$p}{update_action}=\"neve\
+r\";}}\n \n }\n\nsub name2dname\n {\n my (\
+%L)=(@_);\n my ($l, $ml);\n \n foreach my\
+ $pg (keys(%L))\n {\n $l=length ($pg);\n if (\
+ $l>$ml){$ml=$l;}\n }\n $ml+=1;\n forea\
+ch my $pg (keys(%L))\n {\n my $name;\n $l=$ml\
+-length ($pg);\n $name=$pg;\n for ( $b=0; $b<$l; $\
+b++)\n {\n $name .=\" \";\n }\n $L{$pg}{dn\
+ame}=$name;\n }\n return %L;\n }\n\nsub e\
+nv_file2putenv\n {\n my $f=@_[0];\n my $F=n\
+ew FileHandle;\n my $n;\n \n open ($F, \"\
+$f\");\n while (<$F>)\n {\n my $line=$_;\n\
+ my($var, $value)=($_=~/(\\S+)\\=(\\S*)/);\n $ENV{\
+$var}=$value;\n $ENV_SET{$var}=1;\n $n++;\n }\
+\n close ($F);\n return $n;\n }\n\nsub repl\
+ace_line_in_file\n {\n my ($file, $wordin, $wo\
+rdout)=@_;\n my $O=new FileHandle;\n my $I=n\
+ew FileHandle;\n my $l;\n if (!-e $file){ret\
+urn;}\n \n system (\"mv $file $file.old\");\\
+n open ($O, \">$file\");\n open ($I, \"$file\
+.old\");\n while (<$I>)\n {\n $l=$_;\n if \
+(!($l=~/$wordin/)){print $O \"$l\";}\n elsif ( $wo\
+rdout ne \"\"){$l=~s/$wordin/$wordout/g;print $O \\
+"$l\";}\n }\n close ($O);\n close ($I);\
+\n return;\n }\n\nsub add_C_libraries\n {\n \
+ my ($file,$first,@list)=@_;\n \n my $O=new F\
+ileHandle;\n my $I=new FileHandle;\n my ($l,\
+$anchor);\n if (!-e $file){return;}\n \n $\
+anchor=\"#include <$first>\";\n \n system (\"m\
+v $file $file.old\");\n open ($O, \">$file\");\\
+n open ($I, \"$file.old\");\n while (<$I>)\n\
+ {\n $l=$_;\n print $O \"$l\";\n if (!($l=~/$\
+anchor/))\n {\n \n foreach my $lib (@li\
+st)\n {\n print $O \"#incl\
+ude <$lib>\\n\";\n }\n }\n }\
+\n close ($O);\n close ($I);\n return;\n \
+ }\n","use Env;\nuse Cwd;\n@suffix=(\"tmp\", \"t\
+emp\", \"cache\", \"t_coffee\", \"core\", \"tcoffe\
+e\");\n\nif ($#ARGV==-1)\n {\n print \"clean_c\
+ache.pl -file <file to add in -dir> -dir=<dir> -si\
+ze=<value in Mb>\\n0: unlimited -1 always.\\nWill \
+only clean directories matching:[\";\n foreach \
+$k(@suffix){print \"*$k* \";}\n print \"]\\n\";\
+\n exit (EXIT_FAILURE);\n }\n\n$cl=join (\" \"\
+,@ARGV);\nif (($cl=~/\\-no_action/))\n {\n exi\
+t (EXIT_SUCCESS);\n }\n\nif (($cl=~/\\-debug/))\n\
+ {\n $DEBUG=1;\n }\nelse\n {\n $DEBUG=0;\\
+n }\n\nif (($cl=~/\\-dir=(\\S+)/))\n {\n $dir\
+=$1;\n }\nelse\n {\n $dir=\"./\";\n }\n\nif \
+($cl=~/\\-file=(\\S+)/)\n {\n $file=$1;\n }\n\
+else\n {\n $file=0;\n }\n\nif ($cl=~/\\-size=\
+(\\S+)/)\n {\n $max_size=$1;\n }\nelse\n {\n\
+ $max_size=0;#unlimited\n }\nif ($cl=~/\\-forc\
+e/)\n {\n $force=1;\n }\nelse\n {\n $forc\
+e=0;\n }\n\nif ($cl=~/\\-age=(\\S+)/)\n {\n $\
+max_age=$1;\n }\nelse\n {\n $max_age=0;#unlim\
+ited\n }\n\n$max_size*=1000000;\nif ( ! -d $dir)\\
+n {\n print STDERR \"\\nCannot process $dir: d\
+oes not exist \\n\";\n exit (EXIT_FAILURE);\n \
+}\n\nif ( !($dir=~/^\\//))\n {\n $base=cwd();\\
+n $dir=\"$base/$dir\";\n }\n\n$proceed=0;\nfor\
+each $s (@suffix)\n {\n \n if (($dir=~/$s/)\
+){$proceed=1;}\n $s=uc ($s);\n if (($dir=~/$\
+s/)){$proceed=1;}\n }\nif ( $proceed==0)\n {\n \
+ print STDERR \"Clean_cache.pl can only clean dir\
+ectories whose absolute path name contains the fol\
+lowing strings:\";\n foreach $w (@suffix) {prin\
+t STDERR \"$w \";$w=lc($w); print STDERR \"$w \";}\
+\n print STDERR \"\\nCannot process $dir\\n\";\\
+n exit (EXIT_FAILURE);\n }\n\n$name_file=\"$di\
+r/name_file.txt\";\n$size_file=\"$dir/size_file.tx\
+t\";\nif ( $force){&create_ref_file ($dir,$name_fi\
+le,$size_file);}\nif ($file){&add_file ($dir, $nam\
+e_file, $size_file, $file);}\n&clean_dir ($dir, $n\
+ame_file, $size_file, $max_size,$max_age);\nexit (\
+EXIT_SUCCESS);\n\nsub clean_dir \n {\n my ($di\
+r, $name_file, $size_file, $max_size, $max_age)=@_\
+;\n my ($tot_size, $size, $f, $s);\n\n \n $\
+tot_size=&get_tot_size ($dir, $name_file, $size_fi\
+le);\n\n if ( $tot_size<=$max_size){return ;}\n\
+ else {$max_size/=2;}\n \n #recreate the \
+name file in case some temprary files have not bee\
+n properly registered\n &create_ref_file ($dir,\
+ $name_file, $size_file, $max_age);\n \n $new_\
+name_file=&vtmpnam();\n open (R, \"$name_file\"\
+);\n open (W, \">$new_name_file\");\n while \
+(<R>)\n {\n my $line=$_;\n \n ($f, $s)=($line\
+=~/(\\S+) (\\S+)/);\n if ( !($f=~/\\S/)){next;}\n \
+\n elsif ($max_size && $tot_size>=$max_size && !($\
+f=~/name_file/))\n {\n remove ( \"$dir/$f\")\
+;\n $tot_size-=$s;\n }\n elsif ( $max_age &&\
+ -M(\"$dir/$f\")>=$max_age)\n {\n remove ( \\
+"$dir/$f\");\n $tot_size-=$s;\n }\n else\n \
+ {\n print W \"$f $s\\n\";\n }\n }\n \
+ close (R);\n close (W);\n open (F, \">$size\
+_file\");\n print F \"$tot_size\";\n if ( -e\
+ $new_name_file){`mv $new_name_file $name_file`;}\\
+n close (F);\n }\nsub get_tot_size\n {\n m\
+y ($dir, $name_file, $size_file)=@_;\n my $size\
+;\n \n if ( !-d $dir){return 0;}\n if ( !\
+-e $name_file)\n {\n \n &create_ref_file ($di\
+r, $name_file, $size_file);\n }\n open (F,\
+ \"$size_file\");\n $size=<F>;\n close (F);\\
+n chomp ($size);\n return $size;\n }\nsub s\
+ize \n {\n my $f=@_[0];\n\n if ( !-d $f){re\
+turn -s($f);}\n else {return &dir2size($f);}\n \
+ }\nsub dir2size\n {\n my $d=@_[0];\n my ($\
+s, $f);\n \n if ( !-d $d) {return 0;}\n \\
+n foreach $f (&dir2list ($d))\n {\n if ( -\
+d $f){$s+=&dir2size (\"$d/$f\");}\n else {$s+= -s \
+\"$dir/$f\";}\n }\n return $s;\n }\n\nsub\
+ remove \n {\n my $file=@_[0];\n my ($f);\n\
+ \n debug_print( \"--- $file ---\\n\");\n \
+ if (($file eq \".\") || ($file eq \"..\") || ($fi\
+le=~/\\*/)){return EXIT_FAILURE;}\n elsif ( !-d\
+ $file)\n {\n debug_print (\"unlink $file\\n\\
+");\n if (-e $file){unlink ($file);}\n }\n \
+ elsif ( -d $file)\n {\n debug_print (\"+++++\
++++ $file +++++++\\n\");\n foreach $f (&dir2list($\
+file))\n {\n &remove (\"$file/$f\");\n }\n\
+ debug_print (\"rmdir $file\\n\");\n rmdir $file;\\
+n }\n else\n {\n debug_print (\"?????\
+???? $file ????????\\n\");\n }\n return EX\
+IT_SUCCESS;\n }\n\nsub dir2list\n {\n my $dir\
+=@_[0];\n my (@list1, @list2,@list3, $l);\n\n \
+ opendir (DIR,$dir);\n @list1=readdir (DIR);\n\
+ closedir (DIR);\n \n foreach $l (@list1)\
+\n {\n if ( $l ne \".\" && $l ne \"..\"){@lis\
+t2=(@list2, $l);}\n }\n @list3 = sort { (-\
+M \"$dir/$list2[$b]\") <=> (-M \"$dir/$list2[$a]\"\
+)} @list2;\n return @list3;\n \n }\n\nsub d\
+ebug_print\n {\n \n if ($DEBUG==1){print @_\
+;}\n \n }\nsub create_ref_file\n {\n my ($\
+dir,$name_file,$size_file)=@_;\n my ($f, $s, $t\
+ot_size, @l);\n \n if ( !-d $dir){return;}\n\
+ \n @l=&dir2list ($dir);\n open (F, \">$n\
+ame_file\");\n foreach $f (@l)\n {\n $s=&s\
+ize(\"$dir/$f\");\n $tot_size+=$s;\n print F \"$f \
+$s\\n\";\n }\n &myecho ($tot_size, \">$siz\
+e_file\");\n close (F);\n }\nsub add_file \n \
+{\n my ($dir,$name_file,$size_file,$file)=@_;\n\
+ my ($s, $tot_size);\n \n if ( !-d $dir) \
+ {return;}\n if ( !-e \"$dir/$file\" ) {return\
+;}\n if ( !-e $name_file){&create_ref_file ($di\
+r,$name_file,$size_file);}\n \n $s=&siz\
+e(\"$dir/$file\");\n open (F, \">>$name_file\")\
+;\n print F \"$file\\n\";\n close (F);\n\n \
+ $tot_size=&get_tot_size ($dir,$name_file,$size_f\
+ile);\n $tot_size+=$s;\n &myecho ($tot_size,\
+ \">$size_file\");\n \n }\n \nsub myecho\n {\\
+n my ($string, $file)=@_;\n open (ECHO, $fil\
+e) || die;\n print ECHO \"$string\";\n close\
+ (ECHO);\n }\n \n \n \nsub vtmpnam\n {\n \
+my $tmp_file_name;\n $tmp_name_counter++;\n \
+$tmp_file_name=\"tmp_file_for_clean_cache_pdb$$.$t\
+mp_name_counter\";\n $tmp_file_list[$ntmp_file+\
++]=$tmp_file_name;\n if ( -e $tmp_file_name) {r\
+eturn &vtmpnam ();}\n else {return $tmp_file_na\
+me;}\n }\n","\nmy $address=\"http://www.tcoffee.o\
+rg/Projects/Datasets/NatureMethodsDataset.tar.gz\"\
+;\nmy $out=\"NatureMethodsDataset.tar.gz\";\n&url2\
+file ($address,$out);\n\nif ( -e $out)\n {\n \\
+n system (\"gunzip NatureMethodsDataset.tar.gz\\
+");\n system (\"tar -xvf NatureMethodsDataset.t\
+ar\");\n \n print \"Your Data Set is in the \
+Folder NatureMethodsDataset\\n\";\n }\nelse \n {\
+\n print \"Could not Download Dataset --- Web s\
+ite may be down -- Try again later\\n\";\n }\n\n\\
+n\n\nsub url2file\n{\n my ($address, $out, $wge\
+t_arg, $curl_arg)=(@_);\n my ($pg, $flag, $r, $\
+arg, $count);\n \n if (!$CONFIGURATION){&che\
+ck_configuration (\"wget\", \"INTERNET\", \"gzip\"\
+);$CONFIGURATION=1;}\n \n if (&pg_is_install\
+ed (\"wget\")) {$pg=\"wget\"; $flag=\"-O\";$arg=\
+$wget_arg;}\n elsif (&pg_is_installed (\"curl\"\
+)){$pg=\"curl\"; $flag=\"-o\";$arg=$curl_arg;}\n \
+ return system (\"$pg $address $flag $out>/dev/nu\
+ll 2>/dev/null\");\n\n}\n\nsub pg_is_installed\n \
+{\n my @ml=@_;\n my $r, $p, $m;\n my $sup\
+ported=0;\n \n my $p=shift (@ml);\n if ($\
+p=~/::/)\n {\n if (system (\"perl -M$p -e 1\"\
+)==$EXIT_SUCCESS){return 1;}\n else {return 0;}\n \
+ }\n else\n {\n $r=`which $p 2>/dev/nu\
+ll`;\n if ($r eq \"\"){return 0;}\n else {return 1\
+;}\n }\n }\nsub check_configuration \n {\\
+n my @l=@_;\n my $v;\n foreach my $\
+p (@l)\n {\n \n if ( $p eq \"EMAIL\")\n \
+{ \n if ( !($EMAIL=~/@/))\n {\n exit (EX\
+IT_FAILURE);\n }\n }\n elsif( $p eq \"INTER\
+NET\")\n {\n if ( !&check_internet_conne\
+ction())\n {\n exit (EXIT_FAILURE);\n }\n \
+ }\n elsif( $p eq \"wget\")\n {\n if (\
+!&pg_is_installed (\"wget\") && !&pg_is_installed \
+(\"curl\"))\n {\n exit (EXIT_FAILURE);\n }\n \
+ }\n elsif( !(&pg_is_installed ($p)))\n {\
+\n exit (EXIT_FAILURE);\n }\n }\n r\
+eturn 1;\n }\nsub check_internet_connection\n \
+{\n my $internet;\n my $tmp;\n &check_con\
+figuration ( \"wget\"); \n \n $tmp=&vtmpnam \
+();\n \n if (&pg_is_installed (\"wget\
+\")){`wget www.google.com -O$tmp >/dev/null 2>/dev\
+/null`;}\n elsif (&pg_is_installed (\"curl\\
+")){`curl www.google.com -o$tmp >/dev/null 2>/dev/\
+null`;}\n \n if ( !-e $tmp || -s $tmp < 10){\
+$internet=0;}\n else {$internet=1;}\n if (-e\
+ $tmp){unlink $tmp;}\n\n return $internet;\n }\
+\n\nsub vtmpnam\n {\n my $r=rand(100000);\n m\
+y $f=\"file.$r.$$\";\n while (-e $f)\n {\n $\
+f=vtmpnam();\n }\n push (@TMPFILE_LIST, $f);\n r\
+eturn $f;\n }\n\n","\n$t_coffee=\"t_coffee\";\
+\n\nforeach $value ( @ARGV)\n {\n $seq_file=$s\
+eq_file.\" \".$value;\n }\n\n$name=$ARGV[0];\n$na\
+me=~s/\\.[^\\.]*$//;\n$lib_name=\"$name.mocca_lib\\
+";\n$type=`t_coffee $seq_file -get_type -quiet`;\n\
+chop ($type);\n\nif ( $type eq \"PROTEIN\"){$lib_m\
+ode=\"lalign_rs_s_pair -lalign_n_top 20\";}\nelsif\
+ ( $type eq\"DNA\"){$lib_mode=\"lalign_rs_s_dna_pa\
+ir -lalign_n_top 40\";}\n\nif ( !(-e $lib_name))\n\
+ {\n \n $command=\"$t_coffee -mocca -seq_weigh\
+t=no -cosmetic_penalty=0 -mocca_interactive -in $l\
+ib_mode -out_lib $lib_name -infile $seq_file\";\n \
+ \n }\nelsif ( (-e $lib_name))\n {\n $command=\\
+"$t_coffee -mocca -seq_weight=no -cosmetic_penalty\
+=0 -mocca_interactive -in $lib_name -infile $seq_f\
+ile\";\n \n }\n\nsystem ($command);\n\nexit;\n\n\
+","my $WSDL = 'http://www.ebi.ac.uk/Tools/webservi\
+ces/wsdl/WSDaliLite.wsdl';\n\nuse SOAP::Lite;\nuse\
+ Data::Dumper;\nuse Getopt::Long qw(:config no_ign\
+ore_case bundling);\nuse File::Basename;\n\nmy $ch\
+eckInterval = 5;\n\nmy %params=(\n 'async' => \
+'1', # Use async mode and simulate sync mode in cl\
+ient\n );\nGetOptions(\n 'pdb1=s' => \\\
+$params{'sequence1'},\n 'chainid1=s' => \\$para\
+ms{'chainid1'},\n 'pdb2=s' => \\$params{'se\
+quence2'},\n 'chainid2=s' => \\$params{'chainid\
+2'},\n \"help|h\" => \\$help, # Usage info\n \
+ \"async|a\" => \\$async, # Asynchronous submiss\
+ion\n \"polljob\" => \\$polljob, # Get results\
+\n \"status\" => \\$status, # Get status\n \
+\"jobid|j=s\" => \\$jobid, # JobId\n \"email|S\
+=s\" => \\$params{email}, # E-mail address\n \\
+"trace\" => \\$trace, # SOAP messages\n \"\
+sequence=s\" => \\$sequence, # Input PDB\n );\n\
+\nmy $scriptName = basename($0, ());\nif($help) {\\
+n &usage();\n exit(0);\n}\n\nif($trace) {\n \
+ print \"Tracing active\\n\";\n SOAP::Lite->i\
+mport(+trace => 'debug');\n}\n\nmy $soap = SOAP::L\
+ite\n ->service($WSDL)\n ->on_fault(sub {\n \
+ my $soap = shift;\n my $res = shift;\
+\n # Throw an exception for all faults\n \
+ if(ref($res) eq '') {\n die($res);\
+\n } else {\n die($res->faultstr\
+ing);\n }\n return new SOAP::SOM;\n \
+ }\n );\n\nif( !($polljob || $stat\
+us) &&\n !( defined($params{'sequence1'}) && de\
+fined($params{'sequence2'}) )\n ) {\n print \
+STDERR 'Error: bad option combination', \"\\n\";\n\
+ &usage();\n exit(1);\n}\nelsif($polljob && \
+defined($jobid)) {\n print \"Getting results fo\
+r job $jobid\\n\";\n getResults($jobid);\n}\nel\
+sif($status && defined($jobid)) {\n print STDER\
+R \"Getting status for job $jobid\\n\";\n my $r\
+esult = $soap->checkStatus($jobid);\n print STD\
+OUT \"$result\", \"\\n\";\n if($result eq 'DONE\
+') {\n print STDERR \"To get results: $scriptName \
+--polljob --jobid $jobid\\n\";\n }\n}\nelse {\n\
+ if(-f $params{'sequence1'}) {\n $params{'seque\
+nce1'} = read_file($params{'sequence1'});\n }\n\
+ if(-f $params{'sequence2'}) {\n $params{'seque\
+nce2'} = read_file($params{'sequence2'});\n }\n\
+\n my $jobid;\n my $paramsData = SOAP::Data-\
+>name('params')->type(map=>\\%params);\n # For \
+SOAP::Lite 0.60 and earlier parameters are passed \
+directly\n if($SOAP::Lite::VERSION eq '0.60' ||\
+ $SOAP::Lite::VERSION =~ /0\\.[1-5]/) {\n $\
+jobid = $soap->runDaliLite($paramsData);\n }\n \
+ # For SOAP::Lite 0.69 and later parameter handl\
+ing is different, so pass\n # undef's for templ\
+ated params, and then pass the formatted args.\n \
+ else {\n $jobid = $soap->runDaliLite(unde\
+f,\n $paramsData);\n }\n\n if (defin\
+ed($async)) {\n print STDOUT $jobid, \"\\n\";\n \
+ print STDERR \"To check status: $scriptName -\
+-status --jobid $jobid\\n\";\n } else { # Synch\
+ronous mode\n print STDERR \"JobId: $jobid\\
+\n\";\n sleep 1;\n getResults($jobid\
+);\n }\n}\n\nsub clientPoll($) {\n my $jobid\
+ = shift;\n my $result = 'PENDING';\n # Chec\
+k status and wait if not finished\n #print STDE\
+RR \"Checking status: $jobid\\n\";\n while($res\
+ult eq 'RUNNING' || $result eq 'PENDING') {\n \
+ $result = $soap->checkStatus($jobid);\n \
+print STDERR \"$result\\n\";\n if($result e\
+q 'RUNNING' || $result eq 'PENDING') {\n \
+ # Wait before polling again.\n sleep \
+$checkInterval;\n }\n }\n}\n\nsub getRes\
+ults($) {\n $jobid = shift;\n # Check status\
+, and wait if not finished\n clientPoll($jobid)\
+;\n # Use JobId if output file name is not defi\
+ned\n unless(defined($outfile)) {\n $out\
+file=$jobid;\n }\n # Get list of data types\\
+n my $resultTypes = $soap->getResults($jobid);\\
+n # Get the data and write it to a file\n if\
+(defined($outformat)) { # Specified data type\n \
+ my $selResultType;\n foreach my $resul\
+tType (@$resultTypes) {\n if($resultTyp\
+e->{type} eq $outformat) {\n $selRe\
+sultType = $resultType;\n }\n }\\
+n $res=$soap->poll($jobid, $selResultType->\
+{type});\n write_file($outfile.'.'.$selResu\
+ltType->{ext}, $res);\n } else { # Data types a\
+vailable\n # Write a file for each output t\
+ype\n for my $resultType (@$resultTypes){\n\
+ #print \"Getting $resultType->{type}\\\
+n\";\n $res=$soap->poll($jobid, $result\
+Type->{type});\n write_file($outfile.'.\
+'.$resultType->{ext}, $res);\n }\n }\n}\\
+n\nsub read_file($) {\n my $filename = shift;\n\
+ open(FILE, $filename);\n my $content;\n \
+my $buffer;\n while(sysread(FILE, $buffer, 1024\
+)) {\n $content.= $buffer;\n }\n close(FILE)\
+;\n return $content;\n}\n\nsub write_file($$) {\
+\n my ($tmp,$entity) = @_;\n print STDERR \"\
+Creating result file: \".$tmp.\"\\n\";\n unless\
+(open (FILE, \">$tmp\")) {\n return 0;\n }\n \
+ syswrite(FILE, $entity);\n close (FILE);\n \
+return 1;\n}\n\nsub usage {\n print STDERR <<EO\
+F\nDaliLite\n========\n\nPairwise comparison of pr\
+otein structures\n\n[Required]\n\n --pdb1 \
+ : str : PDB ID for structure 1\n --pdb2 \
+ : str : PDB ID for structure 2\n\n\
+[Optional]\n\n --chain1 : str : Cha\
+in identifer in structure 1\n --chain2 \
+ : str : Chain identifer in structure 2\n\n[Gen\
+eral]\n\n -h, --help : : prints t\
+his help text\n -S, --email : str : us\
+er email address\n -a, --async : :\
+ asynchronous submission\n --status \
+: : poll for the status of a job\n --pol\
+ljob : : poll for the results of a jo\
+b\n -j, --jobid : str : jobid for an a\
+synchronous job\n -O, --outfile : str : \
+file name for results (default is jobid)\n --\
+trace : : show SOAP messages being in\
+terchanged \n\nSynchronous job:\n\n The results/e\
+rrors are returned as soon as the job is finished.\
+\n Usage: $scriptName --email <your\\@email> [opt\
+ions] pdbFile [--outfile string]\n Returns: saves\
+ the results to disk\n\nAsynchronous job:\n\n Use\
+ this if you want to retrieve the results at a lat\
+er time. The results \n are stored for up to 24 h\
+ours. \n The asynchronous submission mode is reco\
+mmended when users are submitting \n batch jobs o\
+r large database searches \n Usage: $scriptName -\
+-email <your\\@email> --async [options] pdbFile\n \
+ Returns: jobid\n\n Use the jobid to query for th\
+e status of the job. \n Usage: $scriptName --stat\
+us --jobid <jobId>\n Returns: string indicating t\
+he status of the job:\n DONE - job has finished\
+\n RUNNING - job is running\n NOT_FOUND - jo\
+b cannot be found\n ERROR - the jobs has encoun\
+tered an error\n\n When done, use the jobid to re\
+trieve the status of the job. \n Usage: $scriptNa\
+me --polljob --jobid <jobId> [--outfile string]\n\\
+n[Help]\n\n For more detailed help information re\
+fer to\n http://www.ebi.ac.uk/DaliLite/\nEOF\n;\n\
+}\n","my $WSDL = 'http://www.ebi.ac.uk/Tools/webse\
+rvices/wsdl/WSWUBlast.wsdl';\n\nuse strict;\nuse S\
+OAP::Lite;\nuse Getopt::Long qw(:config no_ignore_\
+case bundling);\nuse File::Basename;\n\nmy $checkI\
+nterval = 15;\n\nmy $numOpts = scalar(@ARGV);\nmy \
+($outfile, $outformat, $help, $async, $polljob, $s\
+tatus, $ids, $jobid, $trace, $sequence);\nmy %para\
+ms= ( # Defaults\n 'async' => 1, # Force int\
+o async mode\n 'exp' => 10.0, # E-value thre\
+shold\n 'numal' => 50, # Maximum number of a\
+lignments\n 'scores' => 100, # Maximum numbe\
+r of scores\n );\nGetOptions( # Map the\
+ options into variables\n \"program|p=s\" =\
+> \\$params{program}, # BLAST program\n \"datab\
+ase|D=s\" => \\$params{database}, # Search data\
+base\n \"matrix|m=s\" => \\$params{matrix}\
+, # Scoring matrix\n \"exp|E=f\" => \\$\
+params{exp}, # E-value threshold\n \"echofilter\
+|e\" => \\$params{echofilter}, # Display filter\
+ed sequence\n \"filter|f=s\" => \\$params{\
+filter}, # Low complexity filter name\n \"align\
+ments|b=i\" => \\$params{numal}, # Number of alig\
+nments\n \"scores|s=i\" => \\$params{score\
+s}, # Number of scores\n \"sensitivity|S=s\" =>\
+ \\$params{sensitivity}, # Search sensitivity\n \
+ \"sort|t=s\" => \\$params{sort}, # Sort hit\
+s by...\n \"stats|T=s\" => \\$params{stat\
+s}, # Scoring statistic to use\n \"strand|d=s\"\
+ => \\$params{strand}, # Strand to use in DNA\
+ vs. DNA search\n \"topcombon|c=i\" => \\$par\
+ams{topcombon}, # Consistent sets of HSPs\n \"o\
+utfile=s\" => \\$outfile, # Output file\n \
+ \"outformat|o=s\" => \\$outformat, # Output for\
+mat\n \"help|h\" => \\$help, # Usage info\
+\n \"async|a\" => \\$async, # Asynchronou\
+s mode\n \"polljob\" => \\$polljob, # Get\
+ results\n \"status\" => \\$status, # Get\
+ job status\n \"ids\" => \\$ids, # \
+Get ids from result\n \"jobid|j=s\" => \\\
+$jobid, # JobId\n \"email=s\" => \\$par\
+ams{email}, # E-mail address\n \"trace\" \
+ => \\$trace, # SOAP trace\n \"sequence=s\" \
+ => \\$sequence, # Query sequence\n );\n\nm\
+y $scriptName = basename($0, ());\nif($help || $nu\
+mOpts == 0) {\n &usage();\n exit(0);\n}\n\ni\
+f($trace){\n print STDERR \"Tracing active\\n\"\
+;\n SOAP::Lite->import(+trace => 'debug');\n}\n\
+\nmy $soap = SOAP::Lite\n ->service($WSDL)\n \
+ ->proxy('http://localhost/',\n #proxy => ['htt\
+p' => 'http://your.proxy.server/'], # HTTP proxy\n\
+ timeout => 600, # HTTP connection timeout\n \
+ )\n ->on_fault(sub { # SOAP fault handler\n \
+ my $soap = shift;\n my $res = shift;\n\
+ # Throw an exception for all faults\n \
+ if(ref($res) eq '') {\n die($res);\n\
+ } else {\n die($res->faultstrin\
+g);\n }\n return new SOAP::SOM;\n \
+ }\n );\n\nif( !($polljob || $status\
+ || $ids) &&\n !( defined($ARGV[0]) || defined(\
+$sequence) )\n ) {\n print STDERR 'Error: ba\
+d option combination', \"\\n\";\n &usage();\n \
+ exit(1);\n}\nelsif($polljob && defined($jobid)) \
+{\n print \"Getting results for job $jobid\\n\"\
+;\n getResults($jobid);\n}\nelsif($status && de\
+fined($jobid)) {\n print STDERR \"Getting statu\
+s for job $jobid\\n\";\n my $result = $soap->ch\
+eckStatus($jobid);\n print STDOUT \"$result\\n\\
+";\n if($result eq 'DONE') {\n print STDERR \"T\
+o get results: $scriptName --polljob --jobid $jobi\
+d\\n\";\n }\n} \nelsif($ids && defined($jobid)\
+) {\n print STDERR \"Getting ids from job $jobi\
+d\\n\";\n getIds($jobid);\n}\nelse {\n # Pre\
+pare input data\n my $content;\n my (@conten\
+ts) = ();\n if(-f $ARGV[0] || $ARGV[0] eq '-') \
+{ \n $content={type=>'sequence',content=>read_file\
+($ARGV[0])}; \n }\n if($sequence) { \n if(-f\
+ $sequence || $sequence eq '-') { \n $content=\
+{type=>'sequence',content=>read_file($ARGV[0])}; \\
+n } else {\n $content={type=>'sequence',conten\
+t=>$sequence};\n }\n }\n push @contents, $co\
+ntent;\n\n # Submit the job\n my $paramsData\
+ = SOAP::Data->name('params')->type(map=>\\%params\
+);\n my $contentData = SOAP::Data->name('conten\
+t')->value(\\@contents);\n # For SOAP::Lite 0.6\
+0 and earlier parameters are passed directly\n \
+if($SOAP::Lite::VERSION eq '0.60' || $SOAP::Lite::\
+VERSION =~ /0\\.[1-5]/) {\n $jobid = $soap-\
+>runWUBlast($paramsData, $contentData);\n }\n \
+ # For SOAP::Lite 0.69 and later parameter handli\
+ng is different, so pass\n # undef's for templa\
+ted params, and then pass the formatted args.\n \
+ else {\n $jobid = $soap->runWUBlast(undef,\
+ undef,\n $paramsData, $contentData);\n }\
+\n\n # Asynchronous mode: output jobid and exit\
+.\n if (defined($async)) {\n print STDOUT $jobi\
+d, \"\\n\";\n print STDERR \"To check statu\
+s: $scriptName --status --jobid $jobid\\n\";\n \
+}\n # Synchronous mode: try to get results\n \
+ else {\n print STDERR \"JobId: $jobid\\n\"\
+;\n sleep 1;\n getResults($jobid);\n\
+ }\n}\n\nsub getIds($) {\n my $jobid = shift\
+;\n my $results = $soap->getIds($jobid);\n f\
+or my $result (@$results){\n print \"$result\\n\";\
+\n }\n}\n\nsub clientPoll($) {\n my $jobid =\
+ shift;\n my $result = 'PENDING';\n # Check \
+status and wait if not finished\n while($result\
+ eq 'RUNNING' || $result eq 'PENDING') {\n \
+$result = $soap->checkStatus($jobid);\n pri\
+nt STDERR \"$result\\n\";\n if($result eq '\
+RUNNING' || $result eq 'PENDING') {\n #\
+ Wait before polling again.\n sleep $ch\
+eckInterval;\n }\n }\n}\n\nsub getResult\
+s($) {\n my $jobid = shift;\n my $res;\n \
+# Check status, and wait if not finished\n clie\
+ntPoll($jobid);\n # Use JobId if output file na\
+me is not defined\n unless(defined($outfile)) {\
+\n $outfile=$jobid;\n }\n # Get list \
+of data types\n my $resultTypes = $soap->getRes\
+ults($jobid);\n # Get the data and write it to \
+a file\n if(defined($outformat)) { # Specified \
+data type\n if($outformat eq 'xml') {$outformat = \
+'toolxml';}\n if($outformat eq 'txt') {$outformat \
+= 'tooloutput';}\n my $selResultType;\n \
+ foreach my $resultType (@$resultTypes) {\n \
+ if($resultType->{type} eq $outformat) {\n \
+ $selResultType = $resultType;\n \
+ }\n }\n $res=$soap->poll($jo\
+bid, $selResultType->{type});\n if($outfile eq '-'\
+) {\n write_file($outfile, $res);\n } else {\\
+n write_file($outfile.'.'.$selResultType->{ext\
+}, $res);\n }\n } else { # Data types available\
+\n # Write a file for each output type\n \
+ for my $resultType (@$resultTypes){\n \
+ #print STDERR \"Getting $resultType->{type}\\n\
+\";\n $res=$soap->poll($jobid, $resultT\
+ype->{type});\n if($outfile eq '-') {\n write\
+_file($outfile, $res);\n } else {\n write_fil\
+e($outfile.'.'.$resultType->{ext}, $res);\n }\\
+n }\n }\n}\n\nsub read_file($) {\n my\
+ $filename = shift;\n my ($content, $buffer);\n\
+ if($filename eq '-') {\n while(sysread(STDIN, \
+$buffer, 1024)) {\n $content .= $buffer;\n }\n\
+ }\n else { # File\n open(FILE, $filename) o\
+r die \"Error: unable to open input file\";\n whil\
+e(sysread(FILE, $buffer, 1024)) {\n $content .\
+= $buffer;\n }\n close(FILE);\n }\n return $\
+content;\n}\n\nsub write_file($$) {\n my ($file\
+name, $data) = @_;\n print STDERR 'Creating res\
+ult file: ' . $filename . \"\\n\";\n if($filena\
+me eq '-') {\n print STDOUT $data;\n }\n els\
+e {\n open(FILE, \">$filename\") or die \"Error: u\
+nable to open output file\";\n syswrite(FILE, $dat\
+a);\n close(FILE);\n }\n}\n\nsub usage {\n p\
+rint STDERR <<EOF\nWU-BLAST\n========\n\nRapid seq\
+uence database search programs utilizing the BLAST\
+ algorithm.\n \n[Required]\n\n --email \
+ : str : user email address \n -p, --program \
+ : str : BLAST program to use: blastn, blastp, b\
+lastx, \n tblastn or t\
+blastx\n -D, --database : str : database to s\
+earch\n seqFile : file : query sequence\
+ data file (\"-\" for STDIN)\n\n[Optional]\n\n -m\
+, --matrix : str : scoring matrix\n -E, --ex\
+p : real : 0<E<= 1000. Statistical significanc\
+e threshold\n for repo\
+rting database sequence matches.\n -e, --echofilt\
+er : : display the filtered query sequence i\
+n the output\n -f, --filter : str : activate\
+s filtering of the query sequence\n -b, --alignme\
+nts : int : number of alignments to be reported\\
+n -s, --scores : int : number of scores to b\
+e reported\n -S, --sensitivity : str :\n -t, --\
+sort : str :\n -T, --stats : str :\n \
+ -d, --strand : str : DNA strand to search w\
+ith in DNA vs. DNA searches \n -c, --topcombon \
+: :\n\n[General] \n\n -h, --help : \
+ : prints this help text\n -a, --async : \
+ : forces to make an asynchronous query\n -\
+-status : : poll for the status of a job\\
+n --polljob : : poll for the results \
+of a job\n -j, --jobid : str : jobid that w\
+as returned when an asynchronous job \n \
+ was submitted.\n -O, --outfile \
+ : str : name of the file results should be writ\
+ten to \n (default is b\
+ased on the jobid; \"-\" for STDOUT)\n -o, --outf\
+ormat : str : txt or xml output (no file is writ\
+ten)\n --trace : : show SOAP messages\
+ being interchanged \n\nSynchronous job:\n\n The \
+results/errors are returned as soon as the job is \
+finished.\n Usage: $scriptName --email <your\\@em\
+ail> [options...] seqFile\n Returns: saves the re\
+sults to disk\n\nAsynchronous job:\n\n Use this i\
+f you want to retrieve the results at a later time\
+. The results \n are stored for up to 24 hours. \\
+n The asynchronous submission mode is recommended\
+ when users are submitting \n batch jobs or large\
+ database searches \n Usage: $scriptName --async \
+--email <your\\@email> [options...] seqFile\n Ret\
+urns : jobid\n\n Use the jobid to query for the s\
+tatus of the job. \n Usage: $scriptName --status \
+--jobid <jobId>\n Returns : string indicating the\
+ status of the job:\n DONE - job has finished\n\
+ RUNNING - job is running\n NOT_FOUND - job \
+cannot be found\n ERROR - the jobs has encounte\
+red an error\n\n When done, use the jobid to retr\
+ieve the status of the job. \n Usage: $scriptName\
+ --polljob --jobid <jobId> [--outfile string]\n R\
+eturns: saves the results to disk\n\n[Help]\n\nFor\
+ more detailed help information refer to \nhttp://\
+www.ebi.ac.uk/blast2/WU-Blast2_Help_frame.html\n \\
+nEOF\n;\n}\n","\nmy $WSDL = 'http://www.ebi.ac.uk/\
+Tools/webservices/wsdl/WSBlastpgp.wsdl';\n\nuse SO\
+AP::Lite;\nuse Getopt::Long qw(:config no_ignore_c\
+ase bundling);\nuse File::Basename;\n\nmy $checkIn\
+terval = 15;\n\nmy %params=(\n 'async' => '1',\
+ # Use async mode and simulate sync mode in client\
+\n );\nGetOptions(\n \"mode=s\" =\
+> \\$params{mode}, # Search mode: PSI-Blast or PHI\
+-Blast\n \"database|d=s\" => \\$params{data\
+base}, # Database to search\n \"matrix|M=s\" \
+ => \\$params{matrix},# Scoring maxtrix\n \"\
+exp|e=f\" => \\$params{exp}, # E-value\n \
+ \"expmulti|h=f\" => \\$params{expmulti}, # \
+E-value\n \"filter|F=s\" => \\$params{fil\
+ter}, # Low complexity filter\n \"dropoff|X=i\"\
+ => \\$params{dropoff}, # Dropoff score\n \
+\"finaldropoff|Z=i\" => \\$params{finaldropoff}, #\
+ Final dropoff score\n \"scores|v=i\" => \
+\\$params{scores}, # Max number of scores\n \"a\
+lign=i\" => \\$params{align}, # Alignment\
+ view\n \"startregion|S=i\" => \\$params{start\
+region}, # Start of region in query\n \"endregi\
+on|H=i\" => \\$params{endregion}, # End of regi\
+on in query\n \"maxpasses|j=i\" => \\$params\
+{maxpasses}, # Number of PSI iterations\n \"ope\
+ngap|G=i\" => \\$params{opengap}, # Gap open \
+penalty\n \"extendgap|E=i\" => \\$params{ext\
+endgap}, # Gap extension penalty\n \"pattern=s\\
+" => \\$params{pattern}, # PHI-BLAST patter\
+n\n \"usagemode|p=s\" => \\$params{usagemode\
+}, # PHI-BLAST program\n \"appxml=s\" =\
+> \\$params{appxml}, # Application XML\n \"sequ\
+ence=s\" => \\$sequence, # Query sequence\n \
+ \"help\" => \\$help, # Usage info\n \\
+"polljob\" => \\$polljob, # Get results\n \
+ \"status\" => \\$status, # Get status\n \
+ \"ids\" => \\$ids, # Get ids from r\
+esult\n \"jobid=s\" => \\$jobid, # Job\
+Id\n \"outfile=s\" => \\$outfile, # Outp\
+ut filename\n \"outformat|o=s\" => \\$outfor\
+mat, # Output file format\n \"async|a\" \
+=> \\$async, # Async submission\n \"email=s\" \
+ => \\$params{email}, # User e-mail address\
+\n \"trace\" => \\$trace, # Show SOA\
+P messages\n );\n\nmy $scriptName = basename($0\
+, ());\nif($help) {\n &usage();\n exit(0);\n\
+}\n\nif ($trace){\n print \"Tracing active\\n\"\
+;\n SOAP::Lite->import(+trace => 'debug');\n}\n\
+\nmy $soap = SOAP::Lite\n ->service($WSDL)\n \
+ ->on_fault(sub {\n my $soap = shift;\n \
+ my $res = shift;\n # Throw an exception\
+ for all faults\n if(ref($res) eq '') {\n \
+ die($res);\n } else {\n \
+ die($res->faultstring);\n }\n retu\
+rn new SOAP::SOM;\n }\n );\n\nif(\
+ !($polljob || $status || $ids) &&\n !( (define\
+d($ARGV[0]) && -f $ARGV[0]) || defined($sequence) \
+)\n ) {\n print STDERR 'Error: bad option co\
+mbination', \"\\n\";\n &usage();\n exit(1);\\
+n}\nelsif($polljob && defined($jobid)) {\n prin\
+t \"Getting results for job $jobid\\n\";\n getR\
+esults($jobid);\n}\nelsif($status && defined($jobi\
+d)) {\n print STDERR \"Getting status for job $\
+jobid\\n\";\n my $result = $soap->checkStatus($\
+jobid);\n print STDOUT $result, \"\\n\";\n i\
+f($result eq 'DONE') {\n print STDERR \"To get res\
+ults: $scriptName --polljob --jobid $jobid\\n\";\n\
+ }\n} \nelsif($ids && defined($jobid)) {\n \
+print STDERR \"Getting ids from job $jobid\\n\";\n\
+ getIds($jobid);\n}\nelse {\n if(-f $ARGV[0]\
+) { \n $content={type=>'sequence', content=>read_f\
+ile($ARGV[0])}; \n }\n if($sequence) { \n if\
+(-f $sequence) {\n $content={type=>'sequence',\
+ content=>read_file($sequence)}; \n } else {\n \
+ $content={type=>'sequence', content=>$sequence};\\
+n }\n }\n push @content, $content;\n\n my\
+ $jobid;\n my $paramsData = SOAP::Data->name('p\
+arams')->type(map=>\\%params);\n my $contentDat\
+a = SOAP::Data->name('content')->value(\\@content)\
+;\n # For SOAP::Lite 0.60 and earlier parameter\
+s are passed directly\n if($SOAP::Lite::VERSION\
+ eq '0.60' || $SOAP::Lite::VERSION =~ /0\\.[1-5]/)\
+ {\n $jobid = $soap->runBlastpgp($paramsDat\
+a, $contentData);\n }\n # For SOAP::Lite 0.6\
+9 and later parameter handling is different, so pa\
+ss\n # undef's for templated params, and then p\
+ass the formatted args.\n else {\n $jobi\
+d = $soap->runBlastpgp(undef, undef,\n $par\
+amsData, $contentData);\n }\n\n if (defined(\
+$async)) {\n print STDOUT $jobid, \"\\n\";\n \
+ print STDERR \"To check status: $scriptName --st\
+atus --jobid $jobid\\n\";\n } else { # Synchron\
+ous mode\n print STDERR \"JobId: $jobid\\n\\
+";\n sleep 1;\n getResults($jobid);\\
+n }\n}\n\nsub getIds($) {\n $jobid = shift;\\
+n my $results = $soap->getIds($jobid);\n for\
+ $result (@$results){\n print \"$result\\n\";\n \
+ }\n}\n\nsub clientPoll($) {\n my $jobid = shif\
+t;\n my $result = 'PENDING';\n # Check statu\
+s and wait if not finished\n #print STDERR \"Ch\
+ecking status: $jobid\\n\";\n while($result eq \
+'RUNNING' || $result eq 'PENDING') {\n $res\
+ult = $soap->checkStatus($jobid);\n print S\
+TDERR \"$result\\n\";\n if($result eq 'RUNN\
+ING' || $result eq 'PENDING') {\n # Wai\
+t before polling again.\n sleep $checkI\
+nterval;\n }\n }\n}\n\nsub getResults($)\
+ {\n $jobid = shift;\n # Check status, and w\
+ait if not finished\n clientPoll($jobid);\n \
+# Use JobId if output file name is not defined\n \
+ unless(defined($outfile)) {\n $outfile=$j\
+obid;\n }\n # Get list of data types\n my\
+ $resultTypes = $soap->getResults($jobid);\n # \
+Get the data and write it to a file\n if(define\
+d($outformat)) { # Specified data type\n my\
+ $selResultType;\n foreach my $resultType (\
+@$resultTypes) {\n if($resultType->{typ\
+e} eq $outformat) {\n $selResultTyp\
+e = $resultType;\n }\n }\n \
+ $res=$soap->poll($jobid, $selResultType->{type})\
+;\n write_file($outfile.'.'.$selResultType-\
+>{ext}, $res);\n } else { # Data types availabl\
+e\n # Write a file for each output type\n \
+ for my $resultType (@$resultTypes){\n \
+ #print \"Getting $resultType->{type}\\n\";\n \
+ $res=$soap->poll($jobid, $resultType->{\
+type});\n write_file($outfile.'.'.$resu\
+ltType->{ext}, $res);\n }\n }\n}\n\nsub \
+read_file($) {\n my $filename = shift;\n ope\
+n(FILE, $filename);\n my $content;\n my $buf\
+fer;\n while(sysread(FILE, $buffer, 1024)) {\n \
+$content.= $buffer;\n }\n close(FILE); \n \
+ return $content;\n}\n\nsub write_file($$) {\n \
+ my ($tmp,$entity) = @_;\n print STDERR \"Creat\
+ing result file: \".$tmp.\"\\n\";\n unless(open\
+ (FILE, \">$tmp\")) {\n return 0;\n }\n sysw\
+rite(FILE, $entity);\n close (FILE);\n retur\
+n 1;\n}\n\nsub usage {\n print STDERR <<EOF\nBl\
+astpgp\n========\n \nThe blastpgp program implem\
+ents the PSI-BLAST and PHI-BLAST variations\nof NC\
+BI BLAST.\n\nFor more detailed help information re\
+fer to\nhttp://www.ebi.ac.uk/blastpgp/blastpsi_hel\
+p_frame.html\n \nBlastpgp specific options:\n\n[Re\
+quired]\n\n --mode : str : search\
+ mode to use: PSI-Blast or PHI-Blast\n -d, --data\
+base : str : protein database to search\n \
+ seqFile : file : query sequence\n\n\
+[Optional]\n\n -M, --matrix : str : sco\
+ring matrix\n -e, --exp : real : Expe\
+ctation value\n -h, --expmulti : real : th\
+reshold (multipass model)\n -F, --filter \
+ : str : filter query sequence with SEG [T,F]\n \
+-m, --align : int : alignment view opti\
+on:\n 0 - pairwise\
+, 1 - M/S identities,\n \
+ 2 - M/S non-identities, 3 - Flat identities,\
+\n 4 - Flat non-id\
+entities\n -G, --opengap : int : cost to\
+ open a gap\n -E, --extendgap : int : cost\
+ to extend a gap\n -g, --gapalign : str :\
+ Gapped [T,F]\n -v, --scores : int : nu\
+mber of scores to be reported\n -j, --maxpasses \
+ : int : number of iterations\n -X, --dropof\
+f : int : Dropoff score\n -Z, --finaldro\
+poff : int : Dropoff for final alignment\n -S\
+, --startregion : int : Start of required reg\
+ion in query\n -H, --endregion : int : End\
+ of required region in query\n -k, --pattern \
+ : str : Hit File (PHI-BLAST only)\n -p, --us\
+agemode : str : Program option (PHI-BLAST o\
+nly):\n blastpgp, \
+patseedp, seedp\n\n[General]\n\n --help \
+ : : prints this help text\n -a, --asyn\
+c : : forces to make an asynchronou\
+s query\n --status : : poll for\
+ the status of a job\n --polljob : \
+ : poll for the results of a job\n --jobid \
+ : str : jobid of an asynchronous job\n \
+ --ids : : get hit identifier\
+s for result \n -O, --outfile : str : na\
+me of the file results should be written to\n \
+ (default is based on t\
+he jobid)\n -o, --outformat : str : txt or\
+ xml output (no file is written)\n --trace \
+ : : show SOAP messages being intercha\
+nged\n\nSynchronous job:\n\n The results/errors a\
+re returned as soon as the job is finished.\n Usa\
+ge: blastpgp.pl --email <your@email> [options...] \
+seqfile\n Returns: saves the results to disk\n\nA\
+synchronous job:\n\n Use this if you want to retr\
+ieve the results at a later time. The results\n a\
+re stored for up to 24 hours.\n The asynchronous \
+submission mode is recommended when users are subm\
+itting\n batch jobs or large database searches\n \
+ Usage: blastpgp.pl --email <your@email> --async [\
+options...] seqFile\n Returns: jobid\n\n Use the\
+ jobid to query for the status of the job.\n Usag\
+e: blastpgp.pl --status --jobid <jobId>\n Returns\
+: string indicating the status of the job\n DON\
+E - job has finished\n RUNNING - job is running\
+\n NOT_FOUND - job cannot be found\n ERROR -\
+ the jobs has encountered an error\n\n When done,\
+ use the jobid to retrieve the results of the job.\
+\n Usage: blastpgp.pl --polljob --jobid <jobId> [\
+--outfile <fileName>]\n Returns: saves the result\
+s to disk\nEOF\n;\n}\n","\n=head1 NAME\n\nncbiblas\
+t_lwp.pl\n\n=head1 DESCRIPTION\n\nNCBI BLAST REST \
+web service Perl client using L<LWP>.\n\nTested wi\
+th:\n\n=over\n\n=item *\nL<LWP> 5.79, L<XML::Simpl\
+e> 2.12 and Perl 5.8.3\n\n=item *\nL<LWP> 5.805, L\
+<XML::Simple> 2.14 and Perl 5.8.7\n\n=item *\nL<LW\
+P> 5.820, L<XML::Simple> 2.18 and Perl 5.10.0 (Ubu\
+ntu 9.04)\n\n=back\n\nFor further information see:\
+\n\n=over\n\n=item *\nL<http://www.ebi.ac.uk/Tools\
+/webservices/services/sss/ncbi_blast_rest>\n\n=ite\
+m *\nL<http://www.ebi.ac.uk/Tools/webservices/tuto\
+rials/perl>\n\n=back\n\n=head1 VERSION\n\n$Id: ncb\
+iblast_lwp.pl 1317 2009-09-03 15:44:11Z hpm $\n\n=\
+cut\n\nuse strict;\nuse warnings;\n\nuse English;\\
+nuse LWP;\nuse XML::Simple;\nuse Getopt::Long qw(:\
+config no_ignore_case bundling);\nuse File::Basena\
+me;\nuse Data::Dumper;\n\nmy $baseUrl = 'http://ww\
+w.ebi.ac.uk/Tools/services/rest/ncbiblast';\n\nmy \
+$checkInterval = 3;\n\nmy $outputLevel = 1;\n\nmy \
+$numOpts = scalar(@ARGV);\nmy %params = ( 'debugLe\
+vel' => 0 );\n\nmy %tool_params = ();\nGetOptions(\
+\n\n # Tool specific options\n 'program|p=s' => \\
+\$tool_params{'program'}, # blastp, blastn, blas\
+tx, etc.\n 'database|D=s' => \\$params{'database'}\
+, # Database(s) to search\n 'matrix|m=s' =\
+> \\$tool_params{'matrix'}, # Scoring martix to\
+ use\n 'exp|E=f' => \\$tool_params{'exp'}, \
+ # E-value threshold\n 'filter|f=s' => \\$too\
+l_params{'filter'}, # Low complexity filter\n '\
+align|A=i' => \\$tool_params{'align'}, # Pa\
+irwise alignment format\n 'scores|s=i' => \\$too\
+l_params{'scores'}, # Number of scores\n 'align\
+ments|n=i' => \\$tool_params{'alignments'}, # Nu\
+mber of alignments\n 'dropoff|d=i' => \\$tool_p\
+arams{'dropoff'}, # Dropoff score\n 'match_sc\
+ores=s' => \\$tool_params{'match_scores'}, # Match\
+/missmatch scores\n 'match|u=i' => \\$params{\
+'match'}, # Match score\n 'mismatch|v=\
+i' => \\$params{'mismatch'}, # Mismatch\
+ score\n 'gapopen|o=i' => \\$tool_params{'gapop\
+en'}, # Open gap penalty\n 'gapext|x=i' =\
+> \\$tool_params{'gapext'}, # Gap extension \
+penality\n 'gapalign|g' => \\$tool_params{'gap\
+align'}, # Optimise gap alignments\n 'stype=s'\
+ => \\$tool_params{'stype'}, # Sequence type\n \
+'seqrange=s' => \\$tool_params{'seqrange'}, # Q\
+uery subsequence\n 'sequence=s' => \\$params{'sequ\
+ence'}, # Query sequence\n 'multifasta' =>\
+ \\$params{'multifasta'}, # Multiple fasta i\
+nput\n\n # Compatability options, old command-line\
+\n 'numal|n=i' => \\$params{'numal'}, #\
+ Number of alignments\n 'opengap|o=i' => \\$para\
+ms{'opengap'}, # Open gap penalty\n 'extendga\
+p|x=i' => \\$params{'extendgap'}, # Gap extensi\
+on penality\n \n # Generic options\n 'email=s' \
+ => \\$params{'email'}, # User e-mail a\
+ddress\n 'title=s' => \\$params{'title'}, \
+ # Job title\n 'outfile=s' => \\$params{\
+'outfile'}, # Output file name\n 'outformat\
+=s' => \\$params{'outformat'}, # Output fil\
+e type\n 'jobid=s' => \\$params{'jobid'}, \
+ # JobId\n 'help|h' => \\$params{'hel\
+p'}, # Usage help\n 'async' => \\
+\$params{'async'}, # Asynchronous submiss\
+ion\n 'polljob' => \\$params{'polljob'}, \
+ # Get results\n 'resultTypes' => \\$params{'\
+resultTypes'}, # Get result types\n 'status' \
+ => \\$params{'status'}, # Get status\\
+n 'params' => \\$params{'params'}, \
+# List input parameters\n 'paramDetail=s' => \\$pa\
+rams{'paramDetail'}, # Get details for paramete\
+r\n 'quiet' => \\$params{'quiet'}, \
+ # Decrease output level\n 'verbose' => \\$\
+params{'verbose'}, # Increase output level\\
+n 'debugLevel=i' => \\$params{'debugLevel'}, \
+# Debug output level\n 'baseUrl=s' => \\$baseU\
+rl, # Base URL for service.\n);\n\
+if ( $params{'verbose'} ) { $outputLevel++ }\nif (\
+ $params{'$quiet'} ) { $outputLevel-- }\n\n&print\
+_debug_message( 'MAIN', 'LWP::VERSION: ' . $LWP::V\
+ERSION,\n 1 );\n\n&print_debug_message( 'MAIN', \"\
+params:\\n\" . Dumper( \\%params ), 11 )\
+;\n&print_debug_message( 'MAIN', \"tool_params:\\n\
+\" . Dumper( \\%tool_params ), 11 );\n\nmy $script\
+Name = basename( $0, () );\n\nif ( $params{'help'}\
+ || $numOpts == 0 ) {\n &usage();\n exit(0);\n}\n\\
+n&print_debug_message( 'MAIN', 'baseUrl: ' . $base\
+Url, 1 );\n\nif (\n !(\n $params{'polljob'}\n \
+ || $params{'resultTypes'}\n || $params{'status'}\
+\n || $params{'params'}\n || $params{'paramDetai\
+l'}\n )\n && !( defined( $ARGV[0] ) || defined( $p\
+arams{'sequence'} ) )\n )\n{\n\n # Bad argument c\
+ombination, so print error message and usage\n pri\
+nt STDERR 'Error: bad option combination', \"\\n\"\
+;\n &usage();\n exit(1);\n}\n\nelsif ( $params{'pa\
+rams'} ) {\n &print_tool_params();\n}\n\nelsif ( $\
+params{'paramDetail'} ) {\n &print_param_details( \
+$params{'paramDetail'} );\n}\n\nelsif ( $params{'s\
+tatus'} && defined( $params{'jobid'} ) ) {\n &prin\
+t_job_status( $params{'jobid'} );\n}\n\nelsif ( $p\
+arams{'resultTypes'} && defined( $params{'jobid'} \
+) ) {\n &print_result_types( $params{'jobid'} );\n\
+}\n\nelsif ( $params{'polljob'} && defined( $param\
+s{'jobid'} ) ) {\n &get_results( $params{'jobid'} \
+);\n}\n\nelse {\n\n # Multiple input sequence mode\
+, assume fasta format.\n if ( $params{'multifasta'\
+} ) {\n &multi_submit_job();\n }\n\n # Entry iden\
+tifier list file.\n elsif (( defined( $params{'seq\
+uence'} ) && $params{'sequence'} =~ m/^\\@/ )\n |\
+| ( defined( $ARGV[0] ) && $ARGV[0] =~ m/^\\@/ ) )\
+\n {\n my $list_filename = $params{'sequence'} ||\
+ $ARGV[0];\n $list_filename =~ s/^\\@//;\n &list\
+_file_submit_job($list_filename);\n }\n\n # Defaul\
+t: single sequence/identifier.\n else {\n\n # Loa\
+d the sequence data and submit.\n &submit_job( &l\
+oad_data() );\n }\n}\n\n=head1 FUNCTIONS\n\n=cut\n\
+\n\n=head2 rest_request()\n\nPerform a REST reques\
+t.\n\n my $response_str = &rest_request($url);\n\\
+n=cut\n\nsub rest_request {\n print_debug_message(\
+ 'rest_request', 'Begin', 11 );\n my $requestUrl =\
+ shift;\n print_debug_message( 'rest_request', 'UR\
+L: ' . $requestUrl, 11 );\n\n # Create a user agen\
+t\n my $ua = LWP::UserAgent->new();\n '$Revision: \
+1317 $' =~ m/(\\d+)/;\n $ua->agent(\"EBI-Sample-Cl\
+ient/$1 ($scriptName; $OSNAME) \" . $ua->agent());\
+\n $ua->env_proxy;\n\n # Perform the request\n my \
+$response = $ua->get($requestUrl);\n print_debug_m\
+essage( 'rest_request', 'HTTP status: ' . $respons\
+e->code,\n 11 );\n\n # Check for HTTP error codes\
+\n if ( $response->is_error ) {\n $response->cont\
+ent() =~ m/<h1>([^<]+)<\\/h1>/;\n die 'http statu\
+s: ' . $response->code . ' ' . $response->message \
+. ' ' . $1;\n }\n print_debug_message( 'rest_requ\
+est', 'End', 11 );\n\n # Return the response data\\
+n return $response->content();\n}\n\n=head2 rest_g\
+et_parameters()\n\nGet list of tool parameter name\
+s.\n\n my (@param_list) = &rest_get_parameters();\
+\n\n=cut\n\nsub rest_get_parameters {\n print_debu\
+g_message( 'rest_get_parameters', 'Begin', 1 );\n \
+my $url = $baseUrl . '/parameters/'\
+;\n my $param_list_xml_str = rest_request($url);\n\
+ my $param_list_xml = XMLin($param_list_xml_st\
+r);\n my (@param_list) = @{ $param_list_xml-\
+>{'id'} };\n print_debug_message( 'rest_get_parame\
+ters', 'End', 1 );\n return (@param_list);\n}\n\n=\
+head2 rest_get_parameter_details()\n\nGet details \
+of a tool parameter.\n\n my $paramDetail = &rest_\
+get_parameter_details($param_name);\n\n=cut\n\nsub\
+ rest_get_parameter_details {\n print_debug_messag\
+e( 'rest_get_parameter_details', 'Begin', 1 );\n m\
+y $parameterId = shift;\n print_debug_message( 're\
+st_get_parameter_details',\n 'parameterId: ' . $p\
+arameterId, 1 );\n my $url = $bas\
+eUrl . '/parameterdetails/' . $parameterId;\n my $\
+param_detail_xml_str = rest_request($url);\n my $p\
+aram_detail_xml = XMLin($param_detail_xml_str)\
+;\n print_debug_message( 'rest_get_parameter_detai\
+ls', 'End', 1 );\n return ($param_detail_xml);\n}\\
+n\n=head2 rest_run()\n\nSubmit a job.\n\n my $job\
+_id = &rest_run($email, $title, \\%params );\n\n=c\
+ut\n\nsub rest_run {\n print_debug_message( 'rest_\
+run', 'Begin', 1 );\n my $email = shift;\n my $ti\
+tle = shift;\n my $params = shift;\n print_debug_\
+message( 'rest_run', 'email: ' . $email, 1 );\n if\
+ ( defined($title) ) {\n print_debug_message( 're\
+st_run', 'title: ' . $title, 1 );\n }\n print_debu\
+g_message( 'rest_run', 'params: ' . Dumper($params\
+), 1 );\n\n # User agent to perform http requests\\
+n my $ua = LWP::UserAgent->new();\n $ua->env_proxy\
+;\n\n # Clean up parameters\n my (%tmp_params) = %\
+{$params};\n $tmp_params{'email'} = $email;\n $tmp\
+_params{'title'} = $title;\n foreach my $param_nam\
+e ( keys(%tmp_params) ) {\n if ( !defined( $tmp_p\
+arams{$param_name} ) ) {\n delete $tmp_params{$p\
+aram_name};\n }\n }\n\n # Submit the job as a POS\
+T\n my $url = $baseUrl . '/run';\n my $response = \
+$ua->post( $url, \\%tmp_params );\n print_debug_me\
+ssage( 'rest_run', 'HTTP status: ' . $response->co\
+de, 11 );\n print_debug_message( 'rest_run',\n 'r\
+equest: ' . $response->request()->content(), 11 );\
+\n\n # Check for HTTP error codes\n if ( $response\
+->is_error ) {\n $response->content() =~ m/<h1>([\
+^<]+)<\\/h1>/;\n die 'http status: ' . $response-\
+>code . ' ' . $response->message . ' ' . $1;\n }\\
+n\n # The job id is returned\n my $job_id = $respo\
+nse->content();\n print_debug_message( 'rest_run',\
+ 'End', 1 );\n return $job_id;\n}\n\n=head2 rest_g\
+et_status()\n\nCheck the status of a job.\n\n my \
+$status = &rest_get_status($job_id);\n\n=cut\n\nsu\
+b rest_get_status {\n print_debug_message( 'rest_g\
+et_status', 'Begin', 1 );\n my $job_id = shift;\n \
+print_debug_message( 'rest_get_status', 'jobid: ' \
+. $job_id, 2 );\n my $status_str = 'UNKNOWN';\n my\
+ $url = $baseUrl . '/status/' . $job_id;\n \
+$status_str = &rest_request($url);\n print_debug_m\
+essage( 'rest_get_status', 'status_str: ' . $statu\
+s_str, 2 );\n print_debug_message( 'rest_get_statu\
+s', 'End', 1 );\n return $status_str;\n}\n\n=head2\
+ rest_get_result_types()\n\nGet list of result typ\
+es for finished job.\n\n my (@result_types) = &re\
+st_get_result_types($job_id);\n\n=cut\n\nsub rest_\
+get_result_types {\n print_debug_message( 'rest_ge\
+t_result_types', 'Begin', 1 );\n my $job_id = shif\
+t;\n print_debug_message( 'rest_get_result_types',\
+ 'jobid: ' . $job_id, 2 );\n my (@resultTypes);\n \
+my $url = $baseUrl . '/result\
+types/' . $job_id;\n my $result_type_list_xml_str \
+= &rest_request($url);\n my $result_type_list_xml \
+ = XMLin($result_type_list_xml_str);\n (@result\
+Types) = @{ $result_type_list_xml->{'type'} };\n p\
+rint_debug_message( 'rest_get_result_types',\n sc\
+alar(@resultTypes) . ' result types', 2 );\n print\
+_debug_message( 'rest_get_result_types', 'End', 1 \
+);\n return (@resultTypes);\n}\n\n=head2 rest_get_\
+result()\n\nGet result data of a specified type fo\
+r a finished job.\n\n my $result = rest_get_resul\
+t($job_id, $result_type);\n\n=cut\n\nsub rest_get_\
+result {\n print_debug_message( 'rest_get_result',\
+ 'Begin', 1 );\n my $job_id = shift;\n my $type \
+= shift;\n print_debug_message( 'rest_get_result',\
+ 'jobid: ' . $job_id, 1 );\n print_debug_message( \
+'rest_get_result', 'type: ' . $type, 1 );\n my \
+$url = $baseUrl . '/result/' . $job_id . '/' . \
+$type;\n my $result = &rest_request($url);\n print\
+_debug_message( 'rest_get_result', length($result)\
+ . ' characters',\n 1 );\n print_debug_message( '\
+rest_get_result', 'End', 1 );\n return $result;\n}\
+\n\n\n=head2 print_debug_message()\n\nPrint debug \
+message at specified debug level.\n\n &print_debu\
+g_message($method_name, $message, $level);\n\n=cut\
+\n\nsub print_debug_message {\n my $function_name \
+= shift;\n my $message = shift;\n my $level \
+ = shift;\n if ( $level <= $params{'debugLe\
+vel'} ) {\n print STDERR '[', $function_name, '()\
+] ', $message, \"\\n\";\n }\n}\n\n=head2 print_too\
+l_params()\n\nPrint list of tool parameters.\n\n \
+&print_tool_params();\n\n=cut\n\nsub print_tool_pa\
+rams {\n print_debug_message( 'print_tool_params',\
+ 'Begin', 1 );\n my (@param_list) = &rest_get_para\
+meters();\n foreach my $param ( sort(@param_list) \
+) {\n print $param, \"\\n\";\n }\n print_debug_me\
+ssage( 'print_tool_params', 'End', 1 );\n}\n\n=hea\
+d2 print_param_details()\n\nPrint details of a too\
+l parameter.\n\n &print_param_details($param_name\
+);\n\n=cut\n\nsub print_param_details {\n print_de\
+bug_message( 'print_param_details', 'Begin', 1 );\\
+n my $paramName = shift;\n print_debug_message( 'p\
+rint_param_details', 'paramName: ' . $paramName, 2\
+ );\n my $paramDetail = &rest_get_parameter_detail\
+s($paramName);\n print $paramDetail->{'name'}, \"\\
+\t\", $paramDetail->{'type'}, \"\\n\";\n print $pa\
+ramDetail->{'description'}, \"\\n\";\n foreach my \
+$value ( @{ $paramDetail->{'values'}->{'value'} } \
+) {\n print $value->{'value'};\n if ( $value->{'\
+defaultValue'} eq 'true' ) {\n print \"\\t\", 'd\
+efault';\n }\n print \"\\n\";\n print \"\\t\", \
+$value->{'label'}, \"\\n\";\n }\n print_debug_mess\
+age( 'print_param_details', 'End', 1 );\n}\n\n=hea\
+d2 print_job_status()\n\nPrint status of a job.\n\\
+n &print_job_status($job_id);\n\n=cut\n\nsub prin\
+t_job_status {\n print_debug_message( 'print_job_s\
+tatus', 'Begin', 1 );\n my $jobid = shift;\n print\
+_debug_message( 'print_job_status', 'jobid: ' . $j\
+obid, 1 );\n if ( $outputLevel > 0 ) {\n print ST\
+DERR 'Getting status for job ', $jobid, \"\\n\";\n\
+ }\n my $result = &rest_get_status($jobid);\n prin\
+t \"$result\\n\";\n if ( $result eq 'FINISHED' && \
+$outputLevel > 0 ) {\n print STDERR \"To get resu\
+lts: $scriptName --polljob --jobid \" . $jobid\n \
+ . \"\\n\";\n }\n print_debug_message( 'print_job\
+_status', 'End', 1 );\n}\n\n=head2 print_result_ty\
+pes()\n\nPrint available result types for a job.\n\
+\n &print_result_types($job_id);\n\n=cut\n\nsub p\
+rint_result_types {\n print_debug_message( 'result\
+_types', 'Begin', 1 );\n my $jobid = shift;\n prin\
+t_debug_message( 'result_types', 'jobid: ' . $jobi\
+d, 1 );\n if ( $outputLevel > 0 ) {\n print STDER\
+R 'Getting result types for job ', $jobid, \"\\n\"\
+;\n }\n my $status = &rest_get_status($jobid);\n i\
+f ( $status eq 'PENDING' || $status eq 'RUNNING' )\
+ {\n print STDERR 'Error: Job status is ', $statu\
+s,\n '. To get result types the job must be fin\
+ished.', \"\\n\";\n }\n else {\n my (@resultTypes\
+) = &rest_get_result_types($jobid);\n if ( $outpu\
+tLevel > 0 ) {\n print STDOUT 'Available result \
+types:', \"\\n\";\n }\n foreach my $resultType (\
+@resultTypes) {\n print STDOUT $resultType->{'id\
+entifier'}, \"\\n\";\n if ( defined( $resultType\
+->{'label'} ) ) {\n print STDOUT \"\\t\", $resu\
+ltType->{'label'}, \"\\n\";\n }\n if ( defined\
+( $resultType->{'description'} ) ) {\n print ST\
+DOUT \"\\t\", $resultType->{'description'}, \"\\n\\
+";\n }\n if ( defined( $resultType->{'mediaTyp\
+e'} ) ) {\n print STDOUT \"\\t\", $resultType->\
+{'mediaType'}, \"\\n\";\n }\n if ( defined( $r\
+esultType->{'fileSuffix'} ) ) {\n print STDOUT \
+\"\\t\", $resultType->{'fileSuffix'}, \"\\n\";\n \
+ }\n }\n if ( $status eq 'FINISHED' && $outputLe\
+vel > 0 ) {\n print STDERR \"\\n\", 'To get resu\
+lts:', \"\\n\",\n \" $scriptName --polljob --\
+jobid \" . $params{'jobid'} . \"\\n\",\n \" $\
+scriptName --polljob --outformat <type> --jobid \"\
+\n . $params{'jobid'} . \"\\n\";\n }\n }\n pr\
+int_debug_message( 'result_types', 'End', 1 );\n}\\
+n\n=head2 submit_job()\n\nSubmit a job to the serv\
+ice.\n\n &submit_job($seq);\n\n=cut\n\nsub submit\
+_job {\n print_debug_message( 'submit_job', 'Begin\
+', 1 );\n\n # Set input sequence\n $tool_params{'s\
+equence'} = shift;\n\n # Load parameters\n &load_p\
+arams();\n\n # Submit the job\n my $jobid = &rest_\
+run( $params{'email'}, $params{'title'}, \\%tool_p\
+arams );\n\n # Simulate sync/async mode\n if ( def\
+ined( $params{'async'} ) ) {\n print STDOUT $jobi\
+d, \"\\n\";\n if ( $outputLevel > 0 ) {\n print\
+ STDERR\n \"To check status: $scriptName --sta\
+tus --jobid $jobid\\n\";\n }\n }\n else {\n if (\
+ $outputLevel > 0 ) {\n print STDERR \"JobId: $j\
+obid\\n\";\n }\n sleep 1;\n &get_results($jobid\
+);\n }\n print_debug_message( 'submit_job', 'End',\
+ 1 );\n}\n\n=head2 multi_submit_job()\n\nSubmit mu\
+ltiple jobs assuming input is a collection of fast\
+a formatted sequences.\n\n &multi_submit_job();\n\
+\n=cut\n\nsub multi_submit_job {\n print_debug_mes\
+sage( 'multi_submit_job', 'Begin', 1 );\n my $jobI\
+dForFilename = 1;\n $jobIdForFilename = 0 if ( def\
+ined( $params{'outfile'} ) );\n my (@filename_list\
+) = ();\n\n # Query sequence\n if ( defined( $ARGV\
+[0] ) ) { # Bare option\n if ( -f $ARGV[0] || \
+$ARGV[0] eq '-' ) { # File\n push( @filename_\
+list, $ARGV[0] );\n }\n }\n if ( $params{'sequenc\
+e'} ) { # Via --sequence\n if (\
+ -f $params{'sequence'} || $params{'sequence'} eq \
+'-' ) { # File\n push( @filename_list, $param\
+s{'sequence'} );\n }\n }\n\n $/ = '>';\n foreach \
+my $filename (@filename_list) {\n open( my $INFIL\
+E, '<', $filename )\n or die \"Error: unable to\
+ open file $filename ($!)\";\n while (<$INFILE>) \
+{\n my $seq = $_;\n $seq =~ s/>$//;\n if ( $\
+seq =~ m/(\\S+)/ ) {\n print STDERR \"Submittin\
+g job for: $1\\n\"\n if ( $outputLevel > 0 );\
+\n $seq = '>' . $seq;\n &print_debug_message\
+( 'multi_submit_job', $seq, 11 );\n &submit_job\
+($seq);\n $params{'outfile'} = undef if ( $jobI\
+dForFilename == 1 );\n }\n }\n close $INFILE;\\
+n }\n print_debug_message( 'multi_submit_job', 'En\
+d', 1 );\n}\n\n=head2 list_file_submit_job()\n\nSu\
+bmit multiple jobs using a file containing a list \
+of entry identifiers as \ninput.\n\n &list_file_s\
+ubmit_job($list_filename)\n\n=cut\n\nsub list_file\
+_submit_job {\n my $filename = shift;\n my\
+ $jobIdForFilename = 1;\n $jobIdForFilename = 0 if\
+ ( defined( $params{'outfile'} ) );\n\n # Iterate \
+over identifiers, submitting each job\n open( my $\
+LISTFILE, '<', $filename )\n or die 'Error: unab\
+le to open file ' . $filename . ' (' . $! . ')';\n\
+ while (<$LISTFILE>) {\n my $line = $_;\n chomp(\
+$line);\n if ( $line ne '' ) {\n &print_debug_m\
+essage( 'list_file_submit_job', 'line: ' . $line, \
+2 );\n if ( $line =~ m/\\w:\\w/ ) { # Check t\
+his is an identifier\n print STDERR \"Submittin\
+g job for: $line\\n\"\n if ( $outputLevel > 0\
+ );\n &submit_job($line);\n }\n else {\n \
+ print STDERR\n\"Warning: line \\\"$line\\\" is no\
+t recognised as an identifier\\n\";\n }\n }\n \
+$params{'outfile'} = undef if ( $jobIdForFilename \
+== 1 );\n }\n close $LISTFILE;\n}\n\n=head2 load_d\
+ata()\n\nLoad sequence data from file or option sp\
+ecified on the command-line.\n\n &load_data();\n\\
+n=cut\n\nsub load_data {\n print_debug_message( 'l\
+oad_data', 'Begin', 1 );\n my $retSeq;\n\n # Query\
+ sequence\n if ( defined( $ARGV[0] ) ) { # Bare\
+ option\n if ( -f $ARGV[0] || $ARGV[0] eq '-' ) {\
+ # File\n $retSeq = &read_file( $ARGV[0] );\n\
+ }\n else { \
+# DB:ID or sequence\n $retSeq = $ARGV[0];\n }\n\
+ }\n if ( $params{'sequence'} ) { \
+ # Via --sequence\n if ( -f $params{'sequence'} \
+|| $params{'sequence'} eq '-' ) { # File\n $r\
+etSeq = &read_file( $params{'sequence'} );\n }\n \
+ else { # DB:ID or sequence\n $retSeq = $para\
+ms{'sequence'};\n }\n }\n print_debug_message( 'l\
+oad_data', 'End', 1 );\n return $retSeq;\n}\n\n=he\
+ad2 load_params()\n\nLoad job parameters from comm\
+and-line options.\n\n &load_params();\n\n=cut\n\n\
+sub load_params {\n print_debug_message( 'load_par\
+ams', 'Begin', 1 );\n\n # Database(s) to search\n \
+my (@dbList) = split /[ ,]/, $params{'database'};\\
+n $tool_params{'database'} = \\@dbList;\n\n # Matc\
+h/missmatch\n if ( $params{'match'} && $params{'mi\
+ssmatch'} ) {\n $tool_params{'match_scores'} =\n \
+ $params{'match'} . ',' . $params{'missmatch'};\\
+n }\n \n # Compatability options, old command-line\
+\n if(!$tool_params{'alignments'} && $params{'numa\
+l'}) {\n $tool_params{'alignments'} = $params{'nu\
+mal'};\n }\n if(!$tool_params{'gapopen'} && $param\
+s{'opengap'}) {\n $tool_params{'gapopen'} = $para\
+ms{'opengap'};\n }\n if(!$tool_params{'gapext'} &&\
+ $params{'extendgap'}) {\n $tool_params{'gapext'}\
+ = $params{'extendgap'};\n }\n\n print_debug_messa\
+ge( 'load_params', 'End', 1 );\n}\n\n=head2 client\
+_poll()\n\nClient-side job polling.\n\n &client_p\
+oll($job_id);\n\n=cut\n\nsub client_poll {\n print\
+_debug_message( 'client_poll', 'Begin', 1 );\n my \
+$jobid = shift;\n my $status = 'PENDING';\n\n my \
+$errorCount = 0;\n while ($status eq 'RUNNING'\n \
+|| $status eq 'PENDING'\n || ( $status eq 'ERROR'\
+ && $errorCount < 2 ) )\n {\n $status = rest_get_\
+status($jobid);\n print STDERR \"$status\\n\" if \
+( $outputLevel > 0 );\n if ( $status eq 'ERROR' )\
+ {\n $errorCount++;\n }\n elsif ( $errorCount \
+> 0 ) {\n $errorCount--;\n }\n if ( $status \
+eq 'RUNNING'\n || $status eq 'PENDING'\n || $s\
+tatus eq 'ERROR' )\n {\n\n # Wait before pollin\
+g again.\n sleep $checkInterval;\n }\n }\n prin\
+t_debug_message( 'client_poll', 'End', 1 );\n retu\
+rn $status;\n}\n\n=head2 get_results()\n\nGet the \
+results for a job identifier.\n\n &get_results($j\
+ob_id);\n\n=cut\n\nsub get_results {\n print_debug\
+_message( 'get_results', 'Begin', 1 );\n my $jobid\
+ = shift;\n print_debug_message( 'get_results', 'j\
+obid: ' . $jobid, 1 );\n\n # Verbose\n if ( $outpu\
+tLevel > 1 ) {\n print 'Getting results for job '\
+, $jobid, \"\\n\";\n }\n\n # Check status, and wai\
+t if not finished\n client_poll($jobid);\n\n # Use\
+ JobId if output file name is not defined\n unless\
+ ( defined( $params{'outfile'} ) ) {\n $params{'o\
+utfile'} = $jobid;\n }\n\n # Get list of data type\
+s\n my (@resultTypes) = rest_get_result_types($job\
+id);\n\n # Get the data and write it to a file\n i\
+f ( defined( $params{'outformat'} ) ) { # Speci\
+fied data type\n my $selResultType;\n foreach my\
+ $resultType (@resultTypes) {\n if ( $resultType\
+->{'identifier'} eq $params{'outformat'} ) {\n \
+$selResultType = $resultType;\n }\n }\n if ( d\
+efined($selResultType) ) {\n my $result =\n \
+rest_get_result( $jobid, $selResultType->{'identif\
+ier'} );\n if ( $params{'outfile'} eq '-' ) {\n \
+ write_file( $params{'outfile'}, $result );\n \
+}\n else {\n write_file(\n $params{'outfi\
+le'} . '.'\n . $selResultType->{'identifier'\
+} . '.'\n . $selResultType->{'fileSuffix'},\\
+n $result\n );\n }\n }\n else {\n die\
+ 'Error: unknown result format \"' . $params{'outf\
+ormat'} . '\"';\n }\n }\n else { # Data types \
+available\n # Write a file for each output \
+type\n for my $resultType (@resultTypes) {\n if\
+ ( $outputLevel > 1 ) {\n print STDERR 'Getting\
+ ', $resultType->{'identifier'}, \"\\n\";\n }\n \
+ my $result = rest_get_result( $jobid, $resultTyp\
+e->{'identifier'} );\n if ( $params{'outfile'} e\
+q '-' ) {\n write_file( $params{'outfile'}, $re\
+sult );\n }\n else {\n write_file(\n $p\
+arams{'outfile'} . '.'\n . $resultType->{'id\
+entifier'} . '.'\n . $resultType->{'fileSuff\
+ix'},\n $result\n );\n }\n }\n }\n print\
+_debug_message( 'get_results', 'End', 1 );\n}\n\n=\
+head2 read_file()\n\nRead a file into a scalar. Th\
+e special filename '-' can be used to read from \n\
+standard input (STDIN).\n\n my $data = &read_file\
+($filename);\n\n=cut\n\nsub read_file {\n print_de\
+bug_message( 'read_file', 'Begin', 1 );\n my $file\
+name = shift;\n print_debug_message( 'read_file', \
+'filename: ' . $filename, 2 );\n my ( $content, $b\
+uffer );\n if ( $filename eq '-' ) {\n while ( sy\
+sread( STDIN, $buffer, 1024 ) ) {\n $content .= \
+$buffer;\n }\n }\n else { # File\n open( my $\
+FILE, '<', $filename )\n or die \"Error: unable\
+ to open input file $filename ($!)\";\n while ( s\
+ysread( $FILE, $buffer, 1024 ) ) {\n $content .=\
+ $buffer;\n }\n close($FILE);\n }\n print_debug_\
+message( 'read_file', 'End', 1 );\n return $conten\
+t;\n}\n\n=head2 write_file()\n\nWrite data to a fi\
+le. The special filename '-' can be used to write \
+to \nstandard output (STDOUT).\n\n &write_file($f\
+ilename, $data);\n\n=cut\n\nsub write_file {\n pri\
+nt_debug_message( 'write_file', 'Begin', 1 );\n my\
+ ( $filename, $data ) = @_;\n print_debug_message(\
+ 'write_file', 'filename: ' . $filename, 2 );\n if\
+ ( $outputLevel > 0 ) {\n print STDERR 'Creating \
+result file: ' . $filename . \"\\n\";\n }\n if ( $\
+filename eq '-' ) {\n print STDOUT $data;\n }\n e\
+lse {\n open( my $FILE, '>', $filename )\n or \
+die \"Error: unable to open output file $filename \
+($!)\";\n syswrite( $FILE, $data );\n close($FIL\
+E);\n }\n print_debug_message( 'write_file', 'End'\
+, 1 );\n}\n\n=head2 usage()\n\nPrint program usage\
+ message.\n\n &usage();\n\n=cut\n\nsub usage {\n \
+print STDERR <<EOF\nNCBI BLAST\n==========\n \nR\
+apid sequence database search programs utilizing t\
+he BLAST algorithm\n \n[Required]\n\n -p, --pr\
+ogram : str : BLAST program to use, see --pa\
+ramDetail program\n -D, --database : str : d\
+atabase(s) to search, space separated. See\n \
+ --paramDetail database\n \
+ --stype : str : query sequence type, s\
+ee --paramDetail stype\n seqFile : fil\
+e : query sequence (\"-\" for STDIN, \\@filename f\
+or\n identifier list \
+file)\n\n[Optional]\n\n -m, --matrix : str \
+ : scoring matrix, see --paramDetail matrix\n -e,\
+ --exp : real : 0<E<= 1000. Statistical s\
+ignificance threshold \n \
+ for reporting database sequence matches.\n -f\
+, --filter : : filter the query sequenc\
+e for low complexity \n \
+ regions, see --paramDetail filter\n -A, --alig\
+n : int : pairwise alignment format, see -\
+-paramDetail align\n -s, --scores : int : \
+number of scores to be reported\n -n, --alignment\
+s : int : number of alignments to report\n -u,\
+ --match : int : Match score (BLASTN only)\
+\n -v, --mismatch : int : Mismatch score (BL\
+ASTN only)\n -o, --gapopen : int : Gap open\
+ penalty\n -x, --gapext : int : Gap extens\
+ion penalty\n -d, --dropoff : int : Drop-of\
+f\n -g, --gapalign : : Optimise gapped a\
+lignments\n --seqrange : str : region wi\
+thin input to use as query\n --multifasta :\
+ : treat input as a set of fasta formatted se\
+quences\n\n[General]\n\n -h, --help : \
+ : prints this help text\n --async : \
+ : forces to make an asynchronous query\n -\
+-email : str : e-mail address\n --titl\
+e : str : title for job\n --status \
+ : : get job status\n --resultTypes : \
+ : get available result types for job\n --\
+polljob : : poll for the status of a job\\
+n --jobid : str : jobid that was retur\
+ned when an asynchronous job \n \
+ was submitted.\n --outfile : st\
+r : file name for results (default is jobid;\n \
+ \"-\" for STDOUT)\n \
+ --outformat : str : result format to retrieve\\
+n --params : : list input parameter\
+s\n --paramDetail : str : display details fo\
+r input parameter\n --quiet : : de\
+crease output\n --verbose : : increa\
+se output\n --trace : : show SOAP \
+messages being interchanged \n \nSynchronous job\
+:\n\n The results/errors are returned as soon as \
+the job is finished.\n Usage: $scriptName --email\
+ <your\\@email> [options...] seqFile\n Returns: r\
+esults as an attachment\n\nAsynchronous job:\n\n \
+Use this if you want to retrieve the results at a \
+later time. The results \n are stored for up to 2\
+4 hours. \n Usage: $scriptName --async --email <\
+your\\@email> [options...] seqFile\n Returns: job\
+id\n\n Use the jobid to query for the status of t\
+he job. If the job is finished, \n it also return\
+s the results/errors.\n Usage: $scriptName --poll\
+job --jobid <jobId> [--outfile string]\n Returns:\
+ string indicating the status of the job and if ap\
+plicable, results \n as an attachment.\n\nFurther\
+ information:\n\n http://www.ebi.ac.uk/Tools/webs\
+ervices/services/sss/ncbi_blast_rest\n http://www\
+.ebi.ac.uk/Tools/webservices/tutorials/perl\n\nSup\
+port/Feedback:\n\n http://www.ebi.ac.uk/support/\\
+nEOF\n}\n\n=head1 FEEDBACK/SUPPORT\n\nPlease conta\
+ct us at L<http://www.ebi.ac.uk/support/> if you h\
+ave any \nfeedback, suggestions or issues with the\
+ service or this client.\n\n=cut\n","\n=head1 NAME\
+\n\nwublast_lwp.pl\n\n=head1 DESCRIPTION\n\nWU-BLA\
+ST REST web service Perl client using L<LWP>.\n\nT\
+ested with:\n\n=over\n\n=item *\nL<LWP> 5.79, L<XM\
+L::Simple> 2.12 and Perl 5.8.3\n\n=item *\nL<LWP> \
+5.805, L<XML::Simple> 2.14 and Perl 5.8.7\n\n=item\
+ *\nL<LWP> 5.820, L<XML::Simple> 2.18 and Perl 5.1\
+0.0 (Ubuntu 9.04)\n\n=back\n\nFor further informat\
+ion see:\n\n=over\n\n=item *\nL<http://www.ebi.ac.\
+uk/Tools/webservices/services/sss/wu_blast_rest>\n\
+\n=item *\nL<http://www.ebi.ac.uk/Tools/webservice\
+s/tutorials/perl>\n\n=back\n\n=head1 VERSION\n\n$I\
+d: wublast_lwp.pl 1317 2009-09-03 15:44:11Z hpm $\\
+n\n=cut\n\nuse strict;\nuse warnings;\n\nuse Engli\
+sh;\nuse LWP;\nuse XML::Simple;\nuse Getopt::Long \
+qw(:config no_ignore_case bundling);\nuse File::Ba\
+sename;\nuse Data::Dumper;\n\nmy $baseUrl = 'http:\
+//www.ebi.ac.uk/Tools/services/rest/wublast';\n\nm\
+y $checkInterval = 3;\n\nmy $outputLevel = 1;\n\nm\
+y $numOpts = scalar(@ARGV);\nmy %params = ( 'debug\
+Level' => 0 );\n\nmy %tool_params = ();\nGetOption\
+s(\n\n # Tool specific options\n 'program|p=s' \
+ => \\$tool_params{'program'}, # BLAST progra\
+m\n 'database|D=s' => \\$params{'database'}, \
+ # Search database\n 'matrix|m=s' => \\$tool\
+_params{'matrix'}, # Scoring matrix\n 'exp|E\
+=f' => \\$tool_params{'exp'}, # E\
+-value threshold\n 'viewfilter|e' => \\$tool_pa\
+rams{'viewfilter'}, # Display filtered sequence\\
+n 'filter|f=s' => \\$tool_params{'filter'}, \
+ # Low complexity filter name\n 'alignments|n=\
+i' => \\$tool_params{'alignments'}, # Number of\
+ alignments\n 'scores|s=i' => \\$tool_params{\
+'scores'}, # Number of scores\n 'sensitivity\
+|S=s' => \\$tool_params{'sensitivity'}, # Search \
+sensitivity\n 'sort|t=s' => \\$tool_params{\
+'sort'}, # Sort hits by...\n 'stats|T=s' \
+ => \\$tool_params{'stats'}, # Scoring \
+statistic to use\n 'strand|d=s' => \\$tool_pa\
+rams{'strand'}, # Strand to use\n 'topcombon\
+|c=i' => \\$tool_params{'topcombon'}, # Consi\
+stent sets of HSPs\n 'align|A=i' => \\$tool_\
+params{'align'}, # Pairwise alignment format\n '\
+stype=s' => \\$tool_params{'stype'}, # Sequence\
+ type 'protein' or 'dna'\n 'sequence=s' => \\$para\
+ms{'sequence'}, # Query sequence file or D\
+B:ID\n 'multifasta' => \\$params{'multifasta'}, \
+ # Multiple fasta input\n\n # Compatability opt\
+ions, old command-line.\n 'echofilter|e' => \\$\
+params{'echofilter'}, # Display filtered sequenc\
+e\n 'b=i' => \\$params{'numal'}, # Number \
+of alignments\n 'appxml=s' => \\$params{'ap\
+pxml'}, # Application XML\n\n # Generic opti\
+ons\n 'email=s' => \\$params{'email'}, \
+ # User e-mail address\n 'title=s' => \\$\
+params{'title'}, # Job title\n 'outfile=s\
+' => \\$params{'outfile'}, # Output fil\
+e name\n 'outformat=s' => \\$params{'outformat'}\
+, # Output file type\n 'jobid=s' => \\$\
+params{'jobid'}, # JobId\n 'help|h' \
+ => \\$params{'help'}, # Usage help\n '\
+async' => \\$params{'async'}, # A\
+synchronous submission\n 'polljob' => \\$par\
+ams{'polljob'}, # Get results\n 'resultType\
+s' => \\$params{'resultTypes'}, # Get result \
+types\n 'status' => \\$params{'status'}, \
+ # Get status\n 'params' => \\$params{\
+'params'}, # List input parameters\n 'para\
+mDetail=s' => \\$params{'paramDetail'}, # Get d\
+etails for parameter\n 'quiet' => \\$param\
+s{'quiet'}, # Decrease output level\n 've\
+rbose' => \\$params{'verbose'}, # Inc\
+rease output level\n 'debugLevel=i' => \\$params{\
+'debugLevel'}, # Debug output level\n 'baseUrl\
+=s' => \\$baseUrl, # Base URL\
+ for service.\n);\nif ( $params{'verbose'} ) { $ou\
+tputLevel++ }\nif ( $params{'$quiet'} ) { $output\
+Level-- }\n\n&print_debug_message( 'MAIN', 'LWP::V\
+ERSION: ' . $LWP::VERSION,\n 1 );\n\n&print_debug_\
+message( 'MAIN', \"params:\\n\" . Dumper( \\%param\
+s ), 11 );\n&print_debug_message( 'MAIN'\
+, \"tool_params:\\n\" . Dumper( \\%tool_params ), \
+11 );\n\nmy $scriptName = basename( $0, () );\n\ni\
+f ( $params{'help'} || $numOpts == 0 ) {\n &usage(\
+);\n exit(0);\n}\n\n&print_debug_message( 'MAIN', \
+'baseUrl: ' . $baseUrl, 1 );\n\nif (\n !(\n $p\
+arams{'polljob'}\n || $params{'resultTypes'}\n |\
+| $params{'status'}\n || $params{'params'}\n || \
+$params{'paramDetail'}\n )\n && !( defined( $ARGV[\
+0] ) || defined( $params{'sequence'} ) )\n )\n{\n\
+\n # Bad argument combination, so print error mess\
+age and usage\n print STDERR 'Error: bad option co\
+mbination', \"\\n\";\n &usage();\n exit(1);\n}\n\n\
+elsif ( $params{'params'} ) {\n &print_tool_params\
+();\n}\n\nelsif ( $params{'paramDetail'} ) {\n &pr\
+int_param_details( $params{'paramDetail'} );\n}\n\\
+nelsif ( $params{'status'} && defined( $params{'jo\
+bid'} ) ) {\n &print_job_status( $params{'jobid'} \
+);\n}\n\nelsif ( $params{'resultTypes'} && defined\
+( $params{'jobid'} ) ) {\n &print_result_types( $p\
+arams{'jobid'} );\n}\n\nelsif ( $params{'polljob'}\
+ && defined( $params{'jobid'} ) ) {\n &get_results\
+( $params{'jobid'} );\n}\n\nelse {\n\n # Multiple \
+input sequence mode, assume fasta format.\n if ( $\
+params{'multifasta'} ) {\n &multi_submit_job();\n\
+ }\n\n # Entry identifier list file.\n elsif (( de\
+fined( $params{'sequence'} ) && $params{'sequence'\
+} =~ m/^\\@/ )\n || ( defined( $ARGV[0] ) && $ARG\
+V[0] =~ m/^\\@/ ) )\n {\n my $list_filename = $pa\
+rams{'sequence'} || $ARGV[0];\n $list_filename =~\
+ s/^\\@//;\n &list_file_submit_job($list_filename\
+);\n }\n\n # Default: single sequence/identifier.\\
+n else {\n\n # Load the sequence data and submit.\
+\n &submit_job( &load_data() );\n }\n}\n\n=head1 \
+FUNCTIONS\n\n=cut\n\n\n=head2 rest_request()\n\nPe\
+rform a REST request.\n\n my $response_str = &res\
+t_request($url);\n\n=cut\n\nsub rest_request {\n p\
+rint_debug_message( 'rest_request', 'Begin', 11 );\
+\n my $requestUrl = shift;\n print_debug_message( \
+'rest_request', 'URL: ' . $requestUrl, 11 );\n\n #\
+ Create a user agent\n my $ua = LWP::UserAgent->ne\
+w();\n '$Revision: 1317 $' =~ m/(\\d+)/;\n $ua->ag\
+ent(\"EBI-Sample-Client/$1 ($scriptName; $OSNAME) \
+\" . $ua->agent());\n $ua->env_proxy;\n\n # Perfor\
+m the request\n my $response = $ua->get($requestUr\
+l);\n print_debug_message( 'rest_request', 'HTTP s\
+tatus: ' . $response->code,\n 11 );\n\n # Check f\
+or HTTP error codes\n if ( $response->is_error ) {\
+\n $response->content() =~ m/<h1>([^<]+)<\\/h1>/;\
+\n die 'http status: ' . $response->code . ' ' . \
+$response->message . ' ' . $1;\n }\n print_debug_\
+message( 'rest_request', 'End', 11 );\n\n # Return\
+ the response data\n return $response->content();\\
+n}\n\n=head2 rest_get_parameters()\n\nGet list of \
+tool parameter names.\n\n my (@param_list) = &res\
+t_get_parameters();\n\n=cut\n\nsub rest_get_parame\
+ters {\n print_debug_message( 'rest_get_parameters\
+', 'Begin', 1 );\n my $url = $baseU\
+rl . '/parameters/';\n my $param_list_xml_str = re\
+st_request($url);\n my $param_list_xml = XMLin\
+($param_list_xml_str);\n my (@param_list) = \
+@{ $param_list_xml->{'id'} };\n print_debug_messag\
+e( 'rest_get_parameters', 'End', 1 );\n return (@p\
+aram_list);\n}\n\n=head2 rest_get_parameter_detail\
+s()\n\nGet details of a tool parameter.\n\n my $p\
+aramDetail = &rest_get_parameter_details($param_na\
+me);\n\n=cut\n\nsub rest_get_parameter_details {\n\
+ print_debug_message( 'rest_get_parameter_details'\
+, 'Begin', 1 );\n my $parameterId = shift;\n print\
+_debug_message( 'rest_get_parameter_details',\n '\
+parameterId: ' . $parameterId, 1 );\n my $url \
+ = $baseUrl . '/parameterdetails/' . $\
+parameterId;\n my $param_detail_xml_str = rest_req\
+uest($url);\n my $param_detail_xml = XMLin($pa\
+ram_detail_xml_str);\n print_debug_message( 'rest_\
+get_parameter_details', 'End', 1 );\n return ($par\
+am_detail_xml);\n}\n\n=head2 rest_run()\n\nSubmit \
+a job.\n\n my $job_id = &rest_run($email, $title,\
+ \\%params );\n\n=cut\n\nsub rest_run {\n print_de\
+bug_message( 'rest_run', 'Begin', 1 );\n my $email\
+ = shift;\n my $title = shift;\n my $params = sh\
+ift;\n print_debug_message( 'rest_run', 'email: ' \
+. $email, 1 );\n if ( defined($title) ) {\n print\
+_debug_message( 'rest_run', 'title: ' . $title, 1 \
+);\n }\n print_debug_message( 'rest_run', 'params:\
+ ' . Dumper($params), 1 );\n\n # User agent to per\
+form http requests\n my $ua = LWP::UserAgent->new(\
+);\n $ua->env_proxy;\n\n # Clean up parameters\n m\
+y (%tmp_params) = %{$params};\n $tmp_params{'email\
+'} = $email;\n $tmp_params{'title'} = $title;\n fo\
+reach my $param_name ( keys(%tmp_params) ) {\n if\
+ ( !defined( $tmp_params{$param_name} ) ) {\n de\
+lete $tmp_params{$param_name};\n }\n }\n\n # Subm\
+it the job as a POST\n my $url = $baseUrl . '/run'\
+;\n my $response = $ua->post( $url, \\%tmp_params \
+);\n print_debug_message( 'rest_run', 'HTTP status\
+: ' . $response->code, 11 );\n print_debug_message\
+( 'rest_run',\n 'request: ' . $response->request(\
+)->content(), 11 );\n\n # Check for HTTP error cod\
+es\n if ( $response->is_error ) {\n $response->co\
+ntent() =~ m/<h1>([^<]+)<\\/h1>/;\n die 'http sta\
+tus: ' . $response->code . ' ' . $response->messag\
+e . ' ' . $1;\n }\n\n # The job id is returned\n \
+my $job_id = $response->content();\n print_debug_m\
+essage( 'rest_run', 'End', 1 );\n return $job_id;\\
+n}\n\n=head2 rest_get_status()\n\nCheck the status\
+ of a job.\n\n my $status = &rest_get_status($job\
+_id);\n\n=cut\n\nsub rest_get_status {\n print_deb\
+ug_message( 'rest_get_status', 'Begin', 1 );\n my \
+$job_id = shift;\n print_debug_message( 'rest_get_\
+status', 'jobid: ' . $job_id, 2 );\n my $status_st\
+r = 'UNKNOWN';\n my $url = $baseUrl . '/sta\
+tus/' . $job_id;\n $status_str = &rest_request($ur\
+l);\n print_debug_message( 'rest_get_status', 'sta\
+tus_str: ' . $status_str, 2 );\n print_debug_messa\
+ge( 'rest_get_status', 'End', 1 );\n return $statu\
+s_str;\n}\n\n=head2 rest_get_result_types()\n\nGet\
+ list of result types for finished job.\n\n my (@\
+result_types) = &rest_get_result_types($job_id);\n\
+\n=cut\n\nsub rest_get_result_types {\n print_debu\
+g_message( 'rest_get_result_types', 'Begin', 1 );\\
+n my $job_id = shift;\n print_debug_message( 'rest\
+_get_result_types', 'jobid: ' . $job_id, 2 );\n my\
+ (@resultTypes);\n my $url = \
+$baseUrl . '/resulttypes/' . $job_id;\n my $result\
+_type_list_xml_str = &rest_request($url);\n my $re\
+sult_type_list_xml = XMLin($result_type_list_x\
+ml_str);\n (@resultTypes) = @{ $result_type_list_x\
+ml->{'type'} };\n print_debug_message( 'rest_get_r\
+esult_types',\n scalar(@resultTypes) . ' result t\
+ypes', 2 );\n print_debug_message( 'rest_get_resul\
+t_types', 'End', 1 );\n return (@resultTypes);\n}\\
+n\n=head2 rest_get_result()\n\nGet result data of \
+a specified type for a finished job.\n\n my $resu\
+lt = rest_get_result($job_id, $result_type);\n\n=c\
+ut\n\nsub rest_get_result {\n print_debug_message(\
+ 'rest_get_result', 'Begin', 1 );\n my $job_id = s\
+hift;\n my $type = shift;\n print_debug_message(\
+ 'rest_get_result', 'jobid: ' . $job_id, 1 );\n pr\
+int_debug_message( 'rest_get_result', 'type: ' . $\
+type, 1 );\n my $url = $baseUrl . '/result/'\
+ . $job_id . '/' . $type;\n my $result = &rest_req\
+uest($url);\n print_debug_message( 'rest_get_resul\
+t', length($result) . ' characters',\n 1 );\n pri\
+nt_debug_message( 'rest_get_result', 'End', 1 );\n\
+ return $result;\n}\n\n\n=head2 print_debug_messag\
+e()\n\nPrint debug message at specified debug leve\
+l.\n\n &print_debug_message($method_name, $messag\
+e, $level);\n\n=cut\n\nsub print_debug_message {\n\
+ my $function_name = shift;\n my $message = \
+shift;\n my $level = shift;\n if ( $level \
+<= $params{'debugLevel'} ) {\n print STDERR '[', \
+$function_name, '()] ', $message, \"\\n\";\n }\n}\\
+n\n=head2 print_tool_params()\n\nPrint list of too\
+l parameters.\n\n &print_tool_params();\n\n=cut\n\
+\nsub print_tool_params {\n print_debug_message( '\
+print_tool_params', 'Begin', 1 );\n my (@param_lis\
+t) = &rest_get_parameters();\n foreach my $param (\
+ sort(@param_list) ) {\n print $param, \"\\n\";\n\
+ }\n print_debug_message( 'print_tool_params', 'En\
+d', 1 );\n}\n\n=head2 print_param_details()\n\nPri\
+nt details of a tool parameter.\n\n &print_param_\
+details($param_name);\n\n=cut\n\nsub print_param_d\
+etails {\n print_debug_message( 'print_param_detai\
+ls', 'Begin', 1 );\n my $paramName = shift;\n prin\
+t_debug_message( 'print_param_details', 'paramName\
+: ' . $paramName, 2 );\n my $paramDetail = &rest_g\
+et_parameter_details($paramName);\n print $paramDe\
+tail->{'name'}, \"\\t\", $paramDetail->{'type'}, \\
+"\\n\";\n print $paramDetail->{'description'}, \"\\
+\n\";\n foreach my $value ( @{ $paramDetail->{'val\
+ues'}->{'value'} } ) {\n print $value->{'value'};\
+\n if ( $value->{'defaultValue'} eq 'true' ) {\n \
+ print \"\\t\", 'default';\n }\n print \"\\n\";\
+\n print \"\\t\", $value->{'label'}, \"\\n\";\n }\
+\n print_debug_message( 'print_param_details', 'En\
+d', 1 );\n}\n\n=head2 print_job_status()\n\nPrint \
+status of a job.\n\n &print_job_status($job_id);\\
+n\n=cut\n\nsub print_job_status {\n print_debug_me\
+ssage( 'print_job_status', 'Begin', 1 );\n my $job\
+id = shift;\n print_debug_message( 'print_job_stat\
+us', 'jobid: ' . $jobid, 1 );\n if ( $outputLevel \
+> 0 ) {\n print STDERR 'Getting status for job ',\
+ $jobid, \"\\n\";\n }\n my $result = &rest_get_sta\
+tus($jobid);\n print \"$result\\n\";\n if ( $resul\
+t eq 'FINISHED' && $outputLevel > 0 ) {\n print S\
+TDERR \"To get results: $scriptName --polljob --jo\
+bid \" . $jobid\n . \"\\n\";\n }\n print_debug_\
+message( 'print_job_status', 'End', 1 );\n}\n\n=he\
+ad2 print_result_types()\n\nPrint available result\
+ types for a job.\n\n &print_result_types($job_id\
+);\n\n=cut\n\nsub print_result_types {\n print_deb\
+ug_message( 'result_types', 'Begin', 1 );\n my $jo\
+bid = shift;\n print_debug_message( 'result_types'\
+, 'jobid: ' . $jobid, 1 );\n if ( $outputLevel > 0\
+ ) {\n print STDERR 'Getting result types for job\
+ ', $jobid, \"\\n\";\n }\n my $status = &rest_get_\
+status($jobid);\n if ( $status eq 'PENDING' || $st\
+atus eq 'RUNNING' ) {\n print STDERR 'Error: Job \
+status is ', $status,\n '. To get result types \
+the job must be finished.', \"\\n\";\n }\n else {\\
+n my (@resultTypes) = &rest_get_result_types($job\
+id);\n if ( $outputLevel > 0 ) {\n print STDOUT\
+ 'Available result types:', \"\\n\";\n }\n forea\
+ch my $resultType (@resultTypes) {\n print STDOU\
+T $resultType->{'identifier'}, \"\\n\";\n if ( d\
+efined( $resultType->{'label'} ) ) {\n print ST\
+DOUT \"\\t\", $resultType->{'label'}, \"\\n\";\n \
+ }\n if ( defined( $resultType->{'description'} \
+) ) {\n print STDOUT \"\\t\", $resultType->{'de\
+scription'}, \"\\n\";\n }\n if ( defined( $res\
+ultType->{'mediaType'} ) ) {\n print STDOUT \"\\
+\t\", $resultType->{'mediaType'}, \"\\n\";\n }\n\
+ if ( defined( $resultType->{'fileSuffix'} ) ) {\
+\n print STDOUT \"\\t\", $resultType->{'fileSuf\
+fix'}, \"\\n\";\n }\n }\n if ( $status eq 'FIN\
+ISHED' && $outputLevel > 0 ) {\n print STDERR \"\
+\\n\", 'To get results:', \"\\n\",\n \" $scri\
+ptName --polljob --jobid \" . $params{'jobid'} . \\
+"\\n\",\n \" $scriptName --polljob --outforma\
+t <type> --jobid \"\n . $params{'jobid'} . \"\\
+\n\";\n }\n }\n print_debug_message( 'result_type\
+s', 'End', 1 );\n}\n\n=head2 submit_job()\n\nSubmi\
+t a job to the service.\n\n &submit_job($seq);\n\\
+n=cut\n\nsub submit_job {\n print_debug_message( '\
+submit_job', 'Begin', 1 );\n\n # Set input sequenc\
+e\n $tool_params{'sequence'} = shift;\n\n # Load p\
+arameters\n &load_params();\n\n # Submit the job\n\
+ my $jobid = &rest_run( $params{'email'}, $params{\
+'title'}, \\%tool_params );\n\n # Simulate sync/as\
+ync mode\n if ( defined( $params{'async'} ) ) {\n \
+ print STDOUT $jobid, \"\\n\";\n if ( $outputLeve\
+l > 0 ) {\n print STDERR\n \"To check status\
+: $scriptName --status --jobid $jobid\\n\";\n }\n\
+ }\n else {\n if ( $outputLevel > 0 ) {\n print\
+ STDERR \"JobId: $jobid\\n\";\n }\n sleep 1;\n \
+&get_results($jobid);\n }\n print_debug_message( '\
+submit_job', 'End', 1 );\n}\n\n=head2 multi_submit\
+_job()\n\nSubmit multiple jobs assuming input is a\
+ collection of fasta formatted sequences.\n\n &mu\
+lti_submit_job();\n\n=cut\n\nsub multi_submit_job \
+{\n print_debug_message( 'multi_submit_job', 'Begi\
+n', 1 );\n my $jobIdForFilename = 1;\n $jobIdForFi\
+lename = 0 if ( defined( $params{'outfile'} ) );\n\
+ my (@filename_list) = ();\n\n # Query sequence\n \
+if ( defined( $ARGV[0] ) ) { # Bare option\n i\
+f ( -f $ARGV[0] || $ARGV[0] eq '-' ) { # File\n\
+ push( @filename_list, $ARGV[0] );\n }\n }\n if\
+ ( $params{'sequence'} ) { # Via\
+ --sequence\n if ( -f $params{'sequence'} || $par\
+ams{'sequence'} eq '-' ) { # File\n push( @fi\
+lename_list, $params{'sequence'} );\n }\n }\n\n $\
+/ = '>';\n foreach my $filename (@filename_list) {\
+\n open( my $INFILE, '<', $filename )\n or die\
+ \"Error: unable to open file $filename ($!)\";\n \
+ while (<$INFILE>) {\n my $seq = $_;\n $seq =~\
+ s/>$//;\n if ( $seq =~ m/(\\S+)/ ) {\n print\
+ STDERR \"Submitting job for: $1\\n\"\n if ( \
+$outputLevel > 0 );\n $seq = '>' . $seq;\n &\
+print_debug_message( 'multi_submit_job', $seq, 11 \
+);\n &submit_job($seq);\n $params{'outfile'}\
+ = undef if ( $jobIdForFilename == 1 );\n }\n }\
+\n close $INFILE;\n }\n print_debug_message( 'mul\
+ti_submit_job', 'End', 1 );\n}\n\n=head2 list_file\
+_submit_job()\n\nSubmit multiple jobs using a file\
+ containing a list of entry identifiers as \ninput\
+.\n\n &list_file_submit_job($list_filename)\n\n=c\
+ut\n\nsub list_file_submit_job {\n my $filename \
+ = shift;\n my $jobIdForFilename = 1;\n $jobI\
+dForFilename = 0 if ( defined( $params{'outfile'} \
+) );\n\n # Iterate over identifiers, submitting ea\
+ch job\n open( my $LISTFILE, '<', $filename )\n \
+or die 'Error: unable to open file ' . $filename .\
+ ' (' . $! . ')';\n while (<$LISTFILE>) {\n my $l\
+ine = $_;\n chomp($line);\n if ( $line ne '' ) {\
+\n &print_debug_message( 'list_file_submit_job',\
+ 'line: ' . $line, 2 );\n if ( $line =~ m/\\w:\\\
+w/ ) { # Check this is an identifier\n print\
+ STDERR \"Submitting job for: $line\\n\"\n if\
+ ( $outputLevel > 0 );\n &submit_job($line);\n \
+ }\n else {\n print STDERR\n\"Warning: line \
+\\\"$line\\\" is not recognised as an identifier\\\
+n\";\n }\n }\n $params{'outfile'} = undef if (\
+ $jobIdForFilename == 1 );\n }\n close $LISTFILE;\\
+n}\n\n=head2 load_data()\n\nLoad sequence data fro\
+m file or option specified on the command-line.\n\\
+n &load_data();\n\n=cut\n\nsub load_data {\n prin\
+t_debug_message( 'load_data', 'Begin', 1 );\n my $\
+retSeq;\n\n # Query sequence\n if ( defined( $ARGV\
+[0] ) ) { # Bare option\n if ( -f $ARGV[0] || \
+$ARGV[0] eq '-' ) { # File\n $retSeq = &read_\
+file( $ARGV[0] );\n }\n else { \
+ # DB:ID or sequence\n $retSeq\
+ = $ARGV[0];\n }\n }\n if ( $params{'sequence'} )\
+ { # Via --sequence\n if ( -f $\
+params{'sequence'} || $params{'sequence'} eq '-' )\
+ { # File\n $retSeq = &read_file( $params{'se\
+quence'} );\n }\n else { # DB:ID or sequence\\
+n $retSeq = $params{'sequence'};\n }\n }\n prin\
+t_debug_message( 'load_data', 'End', 1 );\n return\
+ $retSeq;\n}\n\n=head2 load_params()\n\nLoad job p\
+arameters from command-line options.\n\n &load_pa\
+rams();\n\n=cut\n\nsub load_params {\n print_debug\
+_message( 'load_params', 'Begin', 1 );\n\n # Datab\
+ase(s) to search\n my (@dbList) = split /[ ,]/, $p\
+arams{'database'};\n $tool_params{'database'} = \\\
+@dbList;\n\n # Compatability options, old command-\
+line.\n if(!$tool_params{'viewfilter'} && $params{\
+'echofilter'}) {\n $tool_params{'viewfilter'} = '\
+true';\n }\n if(!$tool_params{'alignments'} && $pa\
+rams{'numal'}) {\n $tool_params{'alignments'} = $\
+params{'numal'};\n }\n # TODO: set alignment forma\
+t option to get NCBI BLAST XML.\n if($params{'appx\
+ml'}) {\n $tool_params{'align'} = '';\n }\n\n pri\
+nt_debug_message( 'load_params', 'End', 1 );\n}\n\\
+n=head2 client_poll()\n\nClient-side job polling.\\
+n\n &client_poll($job_id);\n\n=cut\n\nsub client_\
+poll {\n print_debug_message( 'client_poll', 'Begi\
+n', 1 );\n my $jobid = shift;\n my $status = 'PEN\
+DING';\n\n my $errorCount = 0;\n while ($status eq\
+ 'RUNNING'\n || $status eq 'PENDING'\n || ( $sta\
+tus eq 'ERROR' && $errorCount < 2 ) )\n {\n $stat\
+us = rest_get_status($jobid);\n print STDERR \"$s\
+tatus\\n\" if ( $outputLevel > 0 );\n if ( $statu\
+s eq 'ERROR' ) {\n $errorCount++;\n }\n elsif \
+( $errorCount > 0 ) {\n $errorCount--;\n }\n i\
+f ( $status eq 'RUNNING'\n || $status eq 'PEND\
+ING'\n || $status eq 'ERROR' )\n {\n\n # Wait\
+ before polling again.\n sleep $checkInterval;\n\
+ }\n }\n print_debug_message( 'client_poll', 'End\
+', 1 );\n return $status;\n}\n\n=head2 get_results\
+()\n\nGet the results for a job identifier.\n\n &\
+get_results($job_id);\n\n=cut\n\nsub get_results {\
+\n print_debug_message( 'get_results', 'Begin', 1 \
+);\n my $jobid = shift;\n print_debug_message( 'ge\
+t_results', 'jobid: ' . $jobid, 1 );\n\n # Verbose\
+\n if ( $outputLevel > 1 ) {\n print 'Getting res\
+ults for job ', $jobid, \"\\n\";\n }\n\n # Check s\
+tatus, and wait if not finished\n client_poll($job\
+id);\n\n # Use JobId if output file name is not de\
+fined\n unless ( defined( $params{'outfile'} ) ) {\
+\n $params{'outfile'} = $jobid;\n }\n\n # Get lis\
+t of data types\n my (@resultTypes) = rest_get_res\
+ult_types($jobid);\n\n # Get the data and write it\
+ to a file\n if ( defined( $params{'outformat'} ) \
+) { # Specified data type\n my $selResultType;\
+\n foreach my $resultType (@resultTypes) {\n if\
+ ( $resultType->{'identifier'} eq $params{'outform\
+at'} ) {\n $selResultType = $resultType;\n }\\
+n }\n if ( defined($selResultType) ) {\n my $r\
+esult =\n rest_get_result( $jobid, $selResultT\
+ype->{'identifier'} );\n if ( $params{'outfile'}\
+ eq '-' ) {\n write_file( $params{'outfile'}, $\
+result );\n }\n else {\n write_file(\n \
+$params{'outfile'} . '.'\n . $selResultType-\
+>{'identifier'} . '.'\n . $selResultType->{'\
+fileSuffix'},\n $result\n );\n }\n }\n \
+else {\n die 'Error: unknown result format \"' .\
+ $params{'outformat'} . '\"';\n }\n }\n else { \
+ # Data types available\n # Write a file fo\
+r each output type\n for my $resultType (@resultT\
+ypes) {\n if ( $outputLevel > 1 ) {\n print S\
+TDERR 'Getting ', $resultType->{'identifier'}, \"\\
+\n\";\n }\n my $result = rest_get_result( $job\
+id, $resultType->{'identifier'} );\n if ( $param\
+s{'outfile'} eq '-' ) {\n write_file( $params{'\
+outfile'}, $result );\n }\n else {\n write_\
+file(\n $params{'outfile'} . '.'\n . $re\
+sultType->{'identifier'} . '.'\n . $resultTy\
+pe->{'fileSuffix'},\n $result\n );\n }\n \
+ }\n }\n print_debug_message( 'get_results', 'End'\
+, 1 );\n}\n\n=head2 read_file()\n\nRead a file int\
+o a scalar. The special filename '-' can be used t\
+o read from \nstandard input (STDIN).\n\n my $dat\
+a = &read_file($filename);\n\n=cut\n\nsub read_fil\
+e {\n print_debug_message( 'read_file', 'Begin', 1\
+ );\n my $filename = shift;\n print_debug_message(\
+ 'read_file', 'filename: ' . $filename, 2 );\n my \
+( $content, $buffer );\n if ( $filename eq '-' ) {\
+\n while ( sysread( STDIN, $buffer, 1024 ) ) {\n \
+ $content .= $buffer;\n }\n }\n else { # File\
+\n open( my $FILE, '<', $filename )\n or die \\
+"Error: unable to open input file $filename ($!)\"\
+;\n while ( sysread( $FILE, $buffer, 1024 ) ) {\n\
+ $content .= $buffer;\n }\n close($FILE);\n }\\
+n print_debug_message( 'read_file', 'End', 1 );\n \
+return $content;\n}\n\n=head2 write_file()\n\nWrit\
+e data to a file. The special filename '-' can be \
+used to write to \nstandard output (STDOUT).\n\n \
+&write_file($filename, $data);\n\n=cut\n\nsub writ\
+e_file {\n print_debug_message( 'write_file', 'Beg\
+in', 1 );\n my ( $filename, $data ) = @_;\n print_\
+debug_message( 'write_file', 'filename: ' . $filen\
+ame, 2 );\n if ( $outputLevel > 0 ) {\n print STD\
+ERR 'Creating result file: ' . $filename . \"\\n\"\
+;\n }\n if ( $filename eq '-' ) {\n print STDOUT \
+$data;\n }\n else {\n open( my $FILE, '>', $filen\
+ame )\n or die \"Error: unable to open output f\
+ile $filename ($!)\";\n syswrite( $FILE, $data );\
+\n close($FILE);\n }\n print_debug_message( 'writ\
+e_file', 'End', 1 );\n}\n\n=head2 usage()\n\nPrint\
+ program usage message.\n\n &usage();\n\n=cut\n\n\
+sub usage {\n print STDERR <<EOF\nWU-BLAST\n======\
+==\n \nRapid sequence database search programs u\
+tilizing the BLAST algorithm\n \n[Required]\n\n\
+ -p, --program : str : BLAST program to use\
+, see --paramDetail program\n -D, --database \
+: str : database(s) to search, space separated. S\
+ee\n --paramDetail da\
+tabase\n --stype : str : query sequen\
+ce type, see --paramDetail stype\n seqFile \
+ : file : query sequence (\"-\" for STDIN, \\@\
+filename for\n identi\
+fier list file)\n\n[Optional]\n\n -m, --matrix \
+ : str : scoring matrix, see --paramDetail mat\
+rix\n -e, --exp : real : 0<E<= 1000. Sta\
+tistical significance threshold \n \
+ for reporting database sequence matc\
+hes.\n -e, --viewfilter : : display the fi\
+ltered query sequence\n -f, --filter : str \
+ : filter the query sequence for low complexity \n\
+ regions, see --param\
+Detail filter\n -A, --align : int : pairw\
+ise alignment format, see --paramDetail align\n -\
+s, --scores : int : number of scores to be \
+reported\n -b, --alignments : int : number of \
+alignments to report\n -S, --sensitivity : str \
+: sensitivity of the search, \n \
+ see --paramDetail sensitivity\n -t, --\
+sort : str : sort order for hits, see --para\
+mDetail sort\n -T, --stats : str : statis\
+tical model, see --paramDetail stats\n -d, --stra\
+nd : str : DNA strand to search with,\n \
+ see --paramDetail strand\
+\n -c, --topcombon : str : consistent sets of\
+ HSPs\n --multifasta : : treat input a\
+s a set of fasta formatted sequences\n\n[General]\\
+n\n -h, --help : : prints this help t\
+ext\n --async : : forces to make a\
+n asynchronous query\n --email : str :\
+ e-mail address\n --title : str : titl\
+e for job\n --status : : get job st\
+atus\n --resultTypes : : get available r\
+esult types for job\n --polljob : : \
+poll for the status of a job\n --jobid \
+: str : jobid that was returned when an asynchron\
+ous job \n was submitt\
+ed.\n --outfile : str : file name for re\
+sults (default is jobid;\n \
+ \"-\" for STDOUT)\n --outformat : str \
+ : result format to retrieve\n --params \
+: : list input parameters\n --paramDetai\
+l : str : display details for input parameter\n \
+ --quiet : : decrease output\n \
+--verbose : : increase output\n --tr\
+ace : : show SOAP messages being interc\
+hanged \n \nSynchronous job:\n\n The results/er\
+rors are returned as soon as the job is finished.\\
+n Usage: $scriptName --email <your\\@email> [opti\
+ons...] seqFile\n Returns: results as an attachme\
+nt\n\nAsynchronous job:\n\n Use this if you want \
+to retrieve the results at a later time. The resul\
+ts \n are stored for up to 24 hours. \n Usage: \
+$scriptName --async --email <your\\@email> [option\
+s...] seqFile\n Returns: jobid\n\n Use the jobid\
+ to query for the status of the job. If the job is\
+ finished, \n it also returns the results/errors.\
+\n Usage: $scriptName --polljob --jobid <jobId> [\
+--outfile string]\n Returns: string indicating th\
+e status of the job and if applicable, results \n \
+ as an attachment.\n\nFurther information:\n\n ht\
+tp://www.ebi.ac.uk/Tools/webservices/services/sss/\
+wu_blast_rest\n http://www.ebi.ac.uk/Tools/webser\
+vices/tutorials/perl\n\nSupport/Feedback:\n\n htt\
+p://www.ebi.ac.uk/support/\nEOF\n}\n\n=head1 FEEDB\
+ACK/SUPPORT\n\nPlease contact us at L<http://www.e\
+bi.ac.uk/support/> if you have any \nfeedback, sug\
+gestions or issues with the service or this client\
+.\n\n=cut\n","\n\n\nmy $PROBTRESH = 0.3;# base pai\
+rs below this prob threshold will be ignored\nmy $\
+WEIGHT = 100.0; # float!!\nmy $NUCALPH = \"ACGTUNR\
+YMKSWHBVD\";\nuse vars qw($NUCALPH $WEIGHT);\n\nmy\
+ $myname = basename($0);\n\nuse strict;\nuse warni\
+ngs;\n\nuse File::Basename;\nuse Getopt::Long;\nus\
+e File::Glob ':glob';\nuse File::Spec;\nuse File::\
+Temp qw/ tempfile tempdir /;\n\n\n\n\nsub tcoffeel\
+ib_header($;$)\n{\n my ($nseq, $fd) = @_;\n \
+if (! defined($fd)) {\n $fd = *STDOUT;\n \
+ }\n printf $fd \"! TC_LIB_FORMAT_01\\n\";\n \
+ printf $fd \"%d\\n\", $nseq;\n}\n\n\nsub tcoffeel\
+ib_header_addseq($$;$)\n{\n my ($id, $seq, $fd)\
+ = @_;\n if (! defined($fd)) {\n $fd = *\
+STDOUT;\n }\n printf $fd \"%s %d %s\\n\", $i\
+d, length($seq), $seq;\n}\n\n\nsub tcoffeelib_comm\
+ent($;$)\n{\n my ($comment, $fd) = @_;\n if \
+(! defined($fd)) {\n $fd = *STDOUT;\n }\\
+n printf $fd \"!\" . $comment . \"\\n\";\n}\n\n\
+\nsub tcoffeelib_struct($$$;$)\n{\n my ($nseq, \
+$len, $bpm, $fd) = @_;\n\n if (! defined($fd)) \
+{\n $fd = *STDOUT;\n }\n\n # output b\
+asepair indices with fixed weight\n printf $fd \
+\"#%d %d\\n\", $nseq, $nseq;\n # output basepai\
+rs (only once) and with unit-offset\n for (my $\
+i=0; $i<$len; $i++) {\n for (my $j=$i+1; $j\
+<$len; $j++) {\n if (! defined($bpm->[$\
+i][$j])) {\n print STDERR \"ERROR: \
+\\$bpm->[$i][$j] undefined\\n\";\n }\n \
+ if ($bpm->[$i][$j]>0) {\n \
+ print $fd $i+1;\n print $fd \" \"\
+;\n print $fd $j+1;\n \
+ print $fd \" \" . $bpm->[$i][$j] . \"\\n\";\n \
+ }\n }\n }\n}\n\n\nsub tcoffeeli\
+b_footer(;$)\n{\n my ($fd) = @_;\n if (! def\
+ined($fd)) {\n $fd = *STDOUT;\n }\n p\
+rint $fd \"! SEQ_1_TO_N\\n\";\n}\n\n\n \nsub pl\
+fold($$$)\n{ \n my ($id, $seq, $probtresh) =\
+ @_;\n my (@struct);# return\n my ($templ, $\
+fhtmp, $fnametmp, $cmd, $ctr, $window_size);\n \
+our $ntemp++;\n \n $templ = $myname . \".pid\
+-\" . $$ .$ntemp .\".XXXXXX\";\n ($fhtmp, $fnam\
+etmp) = tempfile($templ, UNLINK => 1); \n print\
+ $fhtmp \">$id\\n$seq\\n\";\n\n # --- init base\
+pair array\n #\n for (my $i=0; $i<length($se\
+q); $i++) {\n for (my $j=$i+1; $j<length($s\
+eq); $j++) {\n $struct[$i][$j]=0;\n \
+ }\n }\n\n\n # --- call rnaplfold and dro\
+p a readme\n #\n $window_size=(length($seq)<\
+70)?length($seq):70;\n $cmd = \"RNAplfold -W $w\
+indow_size < $fnametmp >/dev/null\";\n system($\
+cmd);\n \n if ($? != 0) {\n printf ST\
+DERR \"ERROR: RNAplfold ($cmd) exited with error s\
+tatus %d\\n\", $? >> 8;\n return;\n }\n \
+ #unlink($fnametmp);\n my $fps = sprintf(\"%s\
+_dp.ps\", $id); # check long name\n \n if (!\
+ -s $fps) {\n {\n\n $fps = sprintf(\"%s_dp.ps\
+\", substr($id,0,12)); # check short name\n if (!\
+ -s $fps)\n {\n die(\"couldn't find expected\
+ file $fps\\n\");\n return;\n }\n }\n \
+ }\n\n \n # --- read base pairs from create\
+d postscript\n #\n open(FH, $fps);\n whil\
+e (my $line = <FH>) {\n my ($nti, $ntj, $pr\
+ob);\n chomp($line); \n # lin\
+e: bp bp sqrt-prob ubox\n my @match = ($lin\
+e =~ m/^([0-9]+) +([0-9]+) +([0-9\\.]+) +ubox$/);\\
+n if (scalar(@match)) {\n $nti=$\
+1;\n $ntj=$2;\n $prob=$3*$3;\
+# prob stored as square root\n\n if ($p\
+rob>$probtresh) {\n #printf STDERR \
+\"\\$struct[$nti][$ntj] sqrtprob=$3 prob=$prob > $\
+probtresh\\n\";\n $struct[$nti-1][$\
+ntj-1] = $WEIGHT\n }\n # sto\
+re with zero-offset\n }\n }\n close(F\
+H);\n\n # remove or gzi postscript\n #\n \
+unlink($fps);\n #\n # or gzip\n #$cmd = \\
+"gzip -qf $fps\";\n #system($cmd);\n #if ($?\
+ != 0) {\n # printf STDERR \"ERROR: gzip ($c\
+md) exited with error status %d\\n\", $? >> 8;\n \
+ #}\n\n return \\@struct;\n}\n\n\n\n\n\nsub rn\
+aseqfmt($)\n{\n my ($seq) = @_;\n # remove g\
+aps\n $seq =~ s/-//g;\n # uppercase RNA\n \
+ $seq = uc($seq);\n # T -> U\n $seq =~ s/T/U\
+/g;\n # check for invalid charaters\n $_ = $\
+seq;\n s/[^$NUCALPH]//g;\n return $_;\n}\n\n\
+\n\n\nsub usage(;$)\n{ \n my ($errmsg) = @_;\
+\n if ($errmsg) {\n print STDERR \"ERROR\
+: $errmsg\\n\";\n }\n print STDERR << \"EOF\\
+";\n$myname:\n Creates a T-Coffee RNA structure li\
+brary from RNAplfold prediction.\n See FIXME:citat\
+ion\nUsage:\n $myname -in seq_file -out tcoffee_li\
+b\nEOF\n exit(1);\n}\n\nsub read_fasta_seq \n \
+{\n my $f=$_[0];\n my %hseq;\n my (@seq, \
+@com, @name);\n my ($a, $s,$nseq);\n\n open \
+(F, $f);\n while (<F>)\n {\n $s.=$_;\n \
+ }\n close (F);\n\n \n @name=($s=~/>(\\S\
+*).*\\n[^>]*/g);\n \n @seq =($s=~/>.*.*\\n([\
+^>]*)/g);\n @com =($s=~/>(\\S*)(.*)\\n([^>]*)/g\
+);\n\n\n $nseq=$#name+1;\n \n for ($a=0; $a\
+<$nseq; $a++)\n {\n my $n=$name[$a];\n my $s;\
+\n $hseq{$n}{name}=$n;\n $s=$seq[$a];$s=~s/\\s//g;\
+\n \n $hseq{$n}{seq}=$s;\n $hseq{$n}{com}=$com[$a]\
+;\n }\n return %hseq;\n }\n\n\n\n\n\n\n\n\
+my $fmsq = \"\";\nmy $flib = \"\";\nmy %OPTS;\nmy \
+%seq;\nmy ($id, $nseq, $i);\nmy @nl;\n\nGetOptions\
+(\"in=s\" => \\$fmsq, \"out=s\" => \\$flib);\n\nif\
+ (! -s $fmsq) {\n usage(\"empty or non-existant\
+ file \\\"$fmsq\\\"\")\n}\nif (length($flib)==0) {\
+\n usage(\"empty out-filename\")\n}\n\n\n\n\n\n\
+\n%seq=read_fasta_seq($fmsq);\n\n\n@nl=keys(%seq);\
+\n\n$nseq=$#nl+1;\nopen FD_LIB, \">$flib\" or die \
+\"can't open $flib!\";\ntcoffeelib_header($nseq, *\
+FD_LIB);\nforeach $id (keys (%seq))\n {\n my (\
+$seq, $fmtseq);\n \n $seq = $seq{$id}{seq};\\
+n \n $fmtseq = rnaseqfmt($seq);# check here,\
+ formatting for folding important later\n if (l\
+ength($seq)!=length($fmtseq)) {\n print STD\
+ERR \"ERROR: invalid sequence $id is not an RNA se\
+quence. read seq is: $seq\\n\";\n exit\n \
+ }\n \n tcoffeelib_header_addseq($id, uc($s\
+eq), *FD_LIB);\n }\ntcoffeelib_comment(\"generate\
+d by $myname on \" . localtime(), *FD_LIB);\n\n\n\\
+n$i=0;\nforeach $id (keys (%seq))\n {\n my ($c\
+leanid, $seq, $bpm);\n $seq=$seq{$id}{seq};\n \
+ $cleanid = $id;\n $cleanid =~ s,[/ ],_,g;# ne\
+eded for rnaplfold\n $seq = rnaseqfmt($seq);\n \
+ \n $bpm = plfold($cleanid, rnaseqfmt($seq), \
+$PROBTRESH); \n \n tcoffeelib_struct($\
+i+1, length($seq), $bpm, *FD_LIB);\n $i++;\n}\n\
+\n\ntcoffeelib_footer(*FD_LIB);\nclose FD_LIB;\nex\
+it (0);\n\n","\n\n\n\n\n$cmd=join ' ', @ARGV;\nif \
+($cmd=~/-infile=(\\S+)/){ $seqfile=$1;}\nif ($cmd=\
+~/-outfile=(\\S+)/){ $libfile=$1;}\n\n\n\n%s=read_\
+fasta_seq ($seqfile);\n\nopen (F, \">$libfile\");\\
+nforeach $name (keys (%s))\n {\n my $tclib=\"$\
+name.RNAplfold_tclib\";\n print (F \">$name _F_\
+ $tclib\\n\");\n seq2RNAplfold2tclib ($name, $s\
+{$name}{seq}, $tclib);\n }\nclose (F);\nexit (EXI\
+T_SUCCESS);\n\nsub seq2RNAplfold2tclib\n {\n m\
+y ($name, $seq, $tclib)=@_;\n my ($tmp);\n $\
+n++;\n $tmp=\"tmp4seq2RNAplfold_tclib.$$.$n.pep\
+\";\n open (RF, \">$tmp\");\n print (RF \">$\
+name\\n$seq\\n\");\n close (RF);\n \n sys\
+tem \"t_coffee -other_pg RNAplfold2tclib.pl -in=$t\
+mp -out=$tclib\";\n \n unlink ($tmp);\n r\
+eturn $tclib;\n }\n \n \nsub read_fasta_seq\
+ \n {\n my $f=@_[0];\n my %hseq;\n my (@\
+seq, @com, @name);\n my ($a, $s,$nseq);\n\n \
+open (F, $f);\n while (<F>)\n {\n $s.=$_;\\
+n }\n close (F);\n\n \n @name=($s=~/\
+>(\\S*).*\\n[^>]*/g);\n \n @seq =($s=~/>.*.*\
+\\n([^>]*)/g);\n @com =($s=~/>\\S*(.*)\\n([^>]*\
+)/g);\n\n \n $nseq=$#name+1;\n \n for \
+($a=0; $a<$nseq; $a++)\n {\n my $n=$name[$a];\
+\n $hseq{$n}{name}=$n;\n $hseq{$n}{seq}=$seq[$a];\\
+n $hseq{$n}{com}=$com[$a];\n }\n return %h\
+seq;\n }\n","use Getopt::Long;\nuse File::Path;\n\
+use Env;\nuse FileHandle;\nuse Cwd;\nuse Sys::Host\
+name;\nour $PIDCHILD;\nour $ERROR_DONE;\nour @TMPF\
+ILE_LIST;\nour $EXIT_FAILURE=1;\nour $EXIT_SUCCESS\
+=0;\n\nour $REFDIR=getcwd;\nour $EXIT_SUCCESS=0;\n\
+our $EXIT_FAILURE=1;\n\nour $PROGRAM=\"tc_generic_\
+method.pl\";\nour $CL=$PROGRAM;\n\nour $CLEAN_EXIT\
+_STARTED;\nour $debug_lock=$ENV{\"DEBUG_LOCK\"};\n\
+our $LOCKDIR=$ENV{\"LOCKDIR_4_TCOFFEE\"};\nif (!$L\
+OCKDIR){$LOCKDIR=getcwd();}\nour $ERRORDIR=$ENV{\"\
+ERRORDIR_4_TCOFFEE\"};\nour $ERRORFILE=$ENV{\"ERRO\
+RFILE_4_TCOFFEE\"};\n&set_lock ($$);\nif (isshellp\
+id(getppid())){lock4tc(getppid(), \"LLOCK\", \"LSE\
+T\", \"$$\\n\");}\n \nour $print;\nmy ($fmsq1\
+, $fmsq2, $output, $outfile, $arch, $psv, $hmmtop_\
+home, $trim, $cov, $sample, $mode, $gor_home, $gor\
+_seq, $gor_obs);\n\nGetOptions(\"-in=s\" => \\$fms\
+q1,\"-output=s\" =>\\$output ,\"-out=s\" => \\$out\
+file, \"-arch=s\" => \\$arch,\"-psv=s\" => \\$psv,\
+ \"-hmmtop_home=s\", \\$hmmtop_home,\"-trim=s\" =>\
+\\$trim ,\"-print=s\" =>\\$print,\"-cov=s\" =>\\$c\
+ov , \"-sample=s\" =>\\$sample, \"-mode=s\" =>\\$m\
+ode, \"-gor_home=s\"=>\\$gor_home, \"-gor_seq=s\"=\
+>\\$gor_seq,\"-gor_obs=s\"=>\\$gor_obs);\n\n\nif (\
+!$mode){$mode = \"hmmtop\"}\nelsif ($mode eq \"hmm\
+top\"){;}\nelsif ($mode eq \"gor\"){;}\nelse {myex\
+it(flush_error (\"-mode=$mode is unknown\"));}\n\n\
+\nour $HOME=$ENV{\"HOME\"};\nour $MCOFFEE=($ENV{\"\
+MCOFFEE_4_TCOFFEE\"})?$ENV{\"MCOFFEE_4_TCOFFEE\"}:\
+\"$HOME/.t_coffee/mcoffee\";\n\nif ($mode eq \"hmm\
+top\")\n {\n check_configuration (\"hmmtop\");\
+\n if (-e $arch){$ENV{'HMMTOP_ARCH'}=$arch;}\n \
+ elsif (-e $ENV{HMMTOP_ARCH}){$arch=$ENV{HMMTOP_\
+ARCH};}\n elsif (-e \"$MCOFFEE/hmmtop.arch\"){$\
+arch=$ENV{'HMMTOP_ARCH'}=\"$MCOFFEE/hmmtop.arch\";\
+}\n elsif (-e \"$hmmtop_home/hmmtop.arc\"){$arc\
+h=$ENV{'HMMTOP_ARCH'}=\"$hmmtop_home/hmmtop.arc\";\
+}\n else {myexit(flush_error ( \"Could not find\
+ ARCH file for hmmtop\"));}\n \n \n if (-\
+e $psv){$ENV{'HMMTOP_PSV'}=$psv;}\n elsif (-e $\
+ENV{HMMTOP_PSV}){$psv=$ENV{HMMTOP_PSV};}\n elsi\
+f (-e \"$MCOFFEE/hmmtop.psv\"){$psv=$ENV{'HMMTOP_P\
+SV'}=\"$MCOFFEE/hmmtop.psv\";}\n elsif (-e \"$h\
+mmtop_home/hmmtop.psv\"){$psv=$ENV{'HMMTOP_PSV'}=\\
+"$hmmtop_home/hmmtop.psv\";}\n else {myexit(flu\
+sh_error ( \"Could not find PSV file for hmmtop\")\
+);}\n }\nelsif ($mode eq \"gor\")\n {\n our $\
+GOR_SEQ;\n our $GOR_OBS;\n \n check_confi\
+guration (\"gorIV\");\n if (-e $gor_seq){$GOR_S\
+EQ=$gor_seq;}\n elsif (-e $ENV{GOR_SEQ}){$GOR_S\
+EQ=$ENV{GOR_SEQ};}\n elsif (-e \"$MCOFFEE/New_K\
+S.267.seq\"){$GOR_SEQ=\"$MCOFFEE/New_KS.267.seq\";\
+}\n elsif (-e \"$gor_home/New_KS.267.seq\"){$GO\
+R_SEQ=\"$gor_home/New_KS.267.seq\";}\n else {my\
+exit(flush_error ( \"Could not find SEQ file for g\
+or\"));}\n\n if (-e $gor_obs){$GOR_OBS=$gor_obs\
+;}\n elsif (-e $ENV{GOR_OBS}){$GOR_OBS=$ENV{GOR\
+_OBS};}\n elsif (-e \"$MCOFFEE/New_KS.267.obs\"\
+){$GOR_OBS=\"$MCOFFEE/New_KS.267.obs\";}\n elsi\
+f (-e \"$gor_home/New_KS.267.obs\"){$GOR_OBS=\"$go\
+r_home/New_KS.267.obs\";}\n else {myexit(flush_\
+error ( \"Could not find OBS file for gor\"));}\n \
+ }\n\n\nif ( ! -e $fmsq1){myexit(flush_error (\"Co\
+uld Not Read Input file $fmsq1\"));}\n\n\nmy $fmsq\
+2=vtmpnam();\nmy $fmsq3=vtmpnam();\nmy $tmpfile=vt\
+mpnam();\nmy $predfile=vtmpnam();\n\nif ($trim){$t\
+rim_action=\" +trim _aln_%%$trim\\_K1 \";}\nif ($c\
+ov) {$cov_action= \" +sim_filter _aln_c$cov \";}\n\
+&safe_system(\"t_coffee -other_pg seq_reformat -in\
+ $fmsq1 -action +convert 'BOUJXZ-' $cov_action $tr\
+im_action -output fasta_aln -out $fmsq2\");\nmy (%\
+pred, %seq, %predA);\n\n\n%seq=read_fasta_seq($fms\
+q2);\n%seq=fasta2sample(\\%seq, $sample);\n\nif (1\
+==2 && $mode eq \"hmmtop\" && $output eq \"cons\")\
+\n {\n fasta2hmmtop_cons($outfile,\\%seq);\n \
+}\nelse\n {\n %pred=fasta2pred(\\%seq, $mode);\
+\n %predA=pred2aln (\\%pred, \\%seq);\n \n \
+ \n if (!$output || $output eq \"prediction\")\
+{output_fasta_seq (\\%predA, $outfile);}\n elsi\
+f ($output eq \"color_html\"){pred2color (\\%pred,\
+\\%seq, $outfile);}\n elsif ($output eq \"cons\\
+"){pred2cons($outfile,\\%predA);}\n else {flush\
+_error (\"$output is an unknown output mode\");}\n\
+ }\n\nsub fasta2sample\n {\n my $SR=shift;\n \
+ my $it=shift;\n my %S=%$SR;\n \n my $s\
+eq=index2seq_name (\\%S, 1);\n my $l=length($S{\
+$seq}{seq});\n my @sl=keys(%S);\n my $nseq=$\
+#sl+1;\n my $index=$nseq;\n \n if (!$sample\
+) {return %S;}\n for (my $a=0; $a<$it; $a++)\n \
+ {\n my $newseq=\"\";\n my $nname=\"$seq\\_sam\
+pled_$index\";\n for (my $p=0; $p<$l; $p++)\n {\\
+n my $i=int(rand($nseq));\n \n my $nam\
+e = $sl[$i];\n my $seq=$S{$name}{seq};\n m\
+y $r=substr ($seq, $p, 1);\n $newseq.=$r;\n \
+}\n $S{$nname}{name}=$nname;\n $S{$nname}{seq}=$ne\
+wseq;\n $S{$nname}{com}=\"sampled\";\n $S{$nname}{\
+index}=++$index;\n }\n return %S;\n }\n \
+ \nsub fasta2pred\n {\n my $s=shift;\n \
+my $mode=shift;\n\n if ( $mode eq \"hmmtop\"){r\
+eturn fasta2hmmtop_pred($s);}\n elsif ($mode eq\
+ \"gor\"){return fasta2gor_pred ($s);}\n }\nsub f\
+asta2hmmtop_cons\n {\n my $outfile=shift;\n \
+ my $SR=shift;\n \n my $o = new FileHandle;\\
+n my $i = new FileHandle;\n my $tmp_in =vtmp\
+nam();\n my $tmp_out=vtmpnam();\n my %seq=%$\
+SR;\n my %pred;\n my $N=keys(%seq);\n \n \
+ output_fasta_seq (\\%seq,$tmp_in, \"seq\");\n \
+ `hmmtop -pi=mpred -if=$tmp_in -sf=FAS -pl 2>/dev\
+/null >$tmp_out`;\n open ($o, \">$outfile\");\n\
+ open ($i, \"$tmp_out\");\n while (<$i>)\n \
+ {\n my $l=$_;\n if (($l=~/>HP\\:\\s+(\\d+)\\s+\
+(.*)/)){my $line=\">$2 NSEQ: $N\\n\";print $o \"$l\
+ine\";}\n elsif ( ($l=~/.*pred(.*)/)) {my $line=\\
+"$1\\n\";print $o \"$line\";}\n }\n close \
+($o);\n close ($i);\n return read_fasta_seq(\
+$tmp);\n }\nsub fasta2hmmtop_pred\n {\n my $S\
+R=shift;\n my $o = new FileHandle;\n my $i =\
+ new FileHandle;\n my $tmp =vtmpnam();\n \
+my $tmp_in =vtmpnam();\n my $tmp_out=vtmpnam();\
+\n my %seq=%$SR;\n my %pred;\n \n\n ou\
+tput_fasta_seq (\\%seq,$tmp_in, \"seq\");\n `hm\
+mtop -if=$tmp_in -sf=FAS -pl 2>/dev/null >$tmp_out\
+`;\n open ($o, \">$tmp\");\n open ($i, \"$tm\
+p_out\");\n while (<$i>)\n {\n my $l=$_;\n\
+ if (($l=~/>HP\\:\\s+(\\d+)\\s+(.*)/)){my $line=\"\
+>$2\\n\";print $o \"$line\";}\n elsif ( ($l=~/.*pr\
+ed(.*)/)) {my $line=\"$1\\n\";print $o \"$line\";\
+}\n }\n close ($o);\n close ($i);\n \
+return read_fasta_seq($tmp);\n }\n \n \n \n \
+ \n \n \n\n \nsub fasta2gor_pred\n {\n my $SR\
+=shift;\n my $o = new FileHandle;\n my $i = \
+new FileHandle;\n my $tmp =vtmpnam();\n m\
+y $tmp_in =vtmpnam();\n my $tmp_out=vtmpnam();\\
+n my %seq=%$SR;\n my %pred;\n \n\n out\
+put_fasta_seq (\\%seq,$tmp_in, \"seq\");\n `gor\
+IV -prd $tmp_in -seq $GOR_SEQ -obs $GOR_OBS >$tmp_\
+out`;\n open ($o, \">$tmp\");\n open ($i, \"\
+$tmp_out\");\n while (<$i>)\n {\n my $l=$_\
+;\n\n \n if ( $l=~/>/){print $o \"$l\";}\n elsif (\
+ $l=~/Predicted Sec. Struct./){$l=~s/Predicted Sec\
+. Struct\\.//;print $o \"$l\";}\n }\n clos\
+e ($o);\n close ($i);\n return read_fasta_se\
+q($tmp);\n }\n \n \nsub index2seq_name\n\
+ {\n \n my $SR=shift;\n my $index=shift;\
+\n \n \n my %S=%$SR;\n \n foreach m\
+y $s (%S)\n {\n if ( $S{$s}{index}==$index){r\
+eturn $s;}\n }\n return \"\";\n }\n\nsub \
+pred2cons\n {\n my $outfile=shift;\n my $pr\
+edR=shift;\n my $seq=shift;\n my %P=%$predR;\
+\n my %C;\n my ($s,@r,$nseq);\n my $f= ne\
+w FileHandle;\n\n open ($f, \">$outfile\");\n\n\
+ if (!$seq){$seq=index2seq_name(\\%P,1);}\n \
+foreach my $s (keys(%P))\n {\n $nseq++;\n $st\
+ring= $P{$s}{seq};\n $string = uc $string;\n my @r\
+=split (//,$string);\n for (my $a=0; $a<=$#r; $a++\
+)\n {\n if (($r[$a]=~/[OHICE]/)){$C{$a}{$r[$\
+a]}++;}\n }\n }\n @l=keys(%C);\n \n \
+ \n $s=$P{$seq}{seq};\n print $f \">$seq pr\
+ed based on $nseq\\n\";\n @r=split (//,$s);\n \
+ \n for (my $x=0; $x<=$#r; $x++)\n {\n if\
+ ($r[$x] ne \"-\")\n {\n my $h=$C{$x}{H};\n \
+ my $i=$C{$x}{I};\n my $o=$C{$x}{O};\n \
+my $c=$C{$x}{C};\n my $e=$C{$x}{E};\n my $\
+l=$i+$o;\n \n if ($h>=$i && $h>=$o && $h>=\
+$c && $h>=$e){$r[$x]='H';}\n elsif ($i>=$o && \
+$i>=$c && $i>=$e){$r[$x]='I';}\n elsif ($o>=$c\
+ && $o>=$e){$r[$x]='O';}\n elsif ($c>=$e){$r[$\
+x]='C';}\n else {$r[$x]='E';}\n }\n }\n\
+ $j=join ('', @r);\n print $f \"$j\\n\";\n \
+ close ($f);\n return $j;\n }\n\nsub pred2aln\
+\n {\n my $PR=shift;\n my $AR=shift;\n \\
+n my $f=new FileHandle;\n my %P=%$PR;\n m\
+y %A=%$AR;\n my %PA;\n my $tmp=vtmpnam();\n \
+ my $f= new FileHandle;\n \n open ($f, \">\
+$tmp\");\n foreach my $s (sort{$A{$a}{index}<=>\
+$A{$b}{index}}(keys (%A)))\n {\n my (@list, $\
+seq, @plist, @pseq, $L, $PL, $c, $w);\n my $seq;\n\
+ my $seq=$A{$s}{seq};\n my $pred=$P{$s}{seq};\n $s\
+eq=pred2alnS($P{$s}{seq},$A{$s}{seq});\n print $f \
+\">$s\\n$seq\\n\";\n }\n close ($f);\n \
+return read_fasta_seq ($tmp);\n }\nsub pred2alnS\\
+n {\n my $pred=shift;\n my $aln= shift;\n \
+ my ($j,$a,$b);\n my @P=split (//, $pred);\n \
+ my @A=split (//, $aln);\n for ($a=$b=0;$a<=$#\
+A; $a++)\n {\n if ($A[$a] ne \"-\"){$A[$a]=$P\
+[$b++];}\n }\n if ($b!= ($#P+1)){add_warni\
+ng (\"Could not thread sequence: $b $#P\");}\n \
+\n $j= join ('', @A);\n return $j;\n }\nsub\
+ pred2color\n {\n my $predP=shift;\n my $al\
+nP=shift;\n my $out=shift;\n my $F=new FileH\
+andle;\n my $struc=vtmpnam();\n my $aln=vtmp\
+nam();\n \n\n output_fasta_seq ($alnP, $aln)\
+;\n my %p=%$predP;\n \n open ($F, \">$str\
+uc\");\n \n \n foreach my $s (keys(%p))\n\
+ {\n \n print $F \">$s\\n\";\n my $s=uc($p{$s\
+}{seq});\n \n $s=~s/[Oo]/0/g;\n $s=~s/[Ee]/0/g;\n \
+\n $s=~s/[Ii]/5/g;\n $s=~s/[Cc]/5/g;\n \n $s=~s/[H\
+h]/9/g;\n \n print $F \"$s\\n\";\n }\n clo\
+se ($F);\n \n \n \n safe_system ( \"t_\
+coffee -other_pg seq_reformat -in $aln -struc_in $\
+struc -struc_in_f number_fasta -output color_html \
+-out $out\");\n return;\n }\n \n \nsub di\
+splay_fasta_seq\n {\n my $SR=shift;\n my %S\
+=%$SR;\n \n foreach my $s (sort{$S{$a}{index\
+}<=>$S{$b}{index}}(keys (%S)))\n {\n print ST\
+DERR \">$s\\n$S{$s}{seq}\\n\";\n }\n close\
+ ($f);\n }\nsub output_fasta_seq\n {\n my $SR\
+=shift;\n my $outfile=shift;\n my $mode =shi\
+ft;\n my $f= new FileHandle;\n my %S=%$SR;\n\
+ \n \n open ($f, \">$outfile\");\n for\
+each my $s (sort{$S{$a}{index}<=>$S{$b}{index}}(ke\
+ys (%S)))\n {\n my $seq=$S{$s}{seq};\n if ( $\
+mode eq \"seq\"){$seq=~s/\\-//g;}\n print $f \">$s\
+\\n$seq\\n\";\n }\n close ($f);\n }\n \
+ \nsub read_fasta_seq \n {\n my $f=$_[0];\n \
+ my %hseq;\n my (@seq, @com, @name);\n my (\
+$a, $s,$nseq);\n my $index;\n open (F, $f);\\
+n while (<F>)\n {\n $s.=$_;\n }\n \
+close (F);\n\n \n @name=($s=~/>(\\S*).*\\n[^\
+>]*/g);\n \n @seq =($s=~/>.*.*\\n([^>]*)/g);\
+\n @com =($s=~/>.*(.*)\\n([^>]*)/g);\n\n\n $\
+nseq=$#name+1;\n \n \n for ($a=0; $a<$nseq;\
+ $a++)\n {\n my $n=$name[$a];\n my $s;\n $hse\
+q{$n}{name}=$n;\n $s=$seq[$a];$s=~s/\\s//g;\n $hse\
+q{$n}{index}=++$index;\n $hseq{$n}{seq}=$s;\n $hse\
+q{$n}{com}=$com[$a];\n }\n return %hseq;\n\
+ }\n\n\nsub file2head\n {\n my $file = shift\
+;\n my $size = shift;\n my $f= new FileHandle;\n m\
+y $line;\n open ($f,$file);\n read ($f,$line, $siz\
+e);\n close ($f);\n return $line;\n }\nsub fi\
+le2tail\n {\n my $file = shift;\n my $size = \
+shift;\n my $f= new FileHandle;\n my $line;\n \n o\
+pen ($f,$file);\n seek ($f,$size*-1, 2);\n read ($\
+f,$line, $size);\n close ($f);\n return $line;\n \
+ }\n\n\nsub vtmpnam\n {\n my $r=rand(10000\
+0);\n my $f=\"file.$r.$$\";\n while (-e $f)\n {\\
+n $f=vtmpnam();\n }\n push (@TMPFILE_LIST, $\
+f);\n return $f;\n }\n\nsub myexit\n {\n \
+my $code=@_[0];\n if ($CLEAN_EXIT_STARTED==1){r\
+eturn;}\n else {$CLEAN_EXIT_STARTED=1;}\n ##\
+# ONLY BARE EXIT\n exit ($code);\n }\nsub set_\
+error_lock\n {\n my $name = shift;\n \
+my $pid=$$;\n\n \n &lock4tc ($$,\"LERROR\
+\", \"LSET\", \"$$ -- ERROR: $name $PROGRAM\\n\");\
+\n return;\n }\nsub set_lock\n {\n my \
+$pid=shift;\n my $msg= shift;\n my $p=getppi\
+d();\n &lock4tc ($pid,\"LLOCK\",\"LRESET\",\"$p\
+$msg\\n\");\n }\nsub unset_lock\n {\n \n \
+ my $pid=shift;\n &lock4tc ($pid,\"LLOCK\",\"LR\
+ELEASE\",\"\");\n }\nsub shift_lock\n {\n my \
+$from=shift;\n my $to=shift;\n my $from_type\
+=shift;\n my $to_type=shift;\n my $action=sh\
+ift;\n my $msg;\n \n if (!&lock4tc($from,\
+ $from_type, \"LCHECK\", \"\")){return 0;}\n $m\
+sg=&lock4tc ($from, $from_type, \"LREAD\", \"\");\\
+n &lock4tc ($from, $from_type,\"LRELEASE\", $ms\
+g);\n &lock4tc ($to, $to_type, $action, $msg);\\
+n return;\n }\nsub isshellpid\n {\n my $p=\
+shift;\n if (!lock4tc ($p, \"LLOCK\", \"LCHECK\\
+")){return 0;}\n else\n {\n my $c=lock4tc(\
+$p, \"LLOCK\", \"LREAD\");\n if ( $c=~/-SHELL-/){r\
+eturn 1;}\n }\n return 0;\n }\nsub isroot\
+pid\n {\n if(lock4tc (getppid(), \"LLOCK\", \"\
+LCHECK\")){return 0;}\n else {return 1;}\n }\n\
+sub lock4tc\n {\n my ($pid,$type,$action,$value)\
+=@_;\n my $fname;\n my $host=hostname;\n \n \
+ if ($type eq \"LLOCK\"){$fname=\"$LOCKDIR/.$pid.\
+$host.lock4tcoffee\";}\n elsif ( $type eq \"LERR\
+OR\"){ $fname=\"$LOCKDIR/.$pid.$host.error4tcoffee\
+\";}\n elsif ( $type eq \"LWARNING\"){ $fname=\"\
+$LOCKDIR/.$pid.$host.warning4tcoffee\";}\n \n \
+if ($debug_lock)\n {\n print STDERR \"\\\
+n\\t---lock4tc(tcg): $action => $fname =>$value (R\
+D: $LOCKDIR)\\n\";\n }\n\n if ($action eq\
+ \"LCHECK\") {return -e $fname;}\n elsif ($actio\
+n eq \"LREAD\"){return file2string($fname);}\n e\
+lsif ($action eq \"LSET\") {return string2file ($v\
+alue, $fname, \">>\");}\n elsif ($action eq \"LR\
+ESET\") {return string2file ($value, $fname, \">\"\
+);}\n elsif ($action eq \"LRELEASE\") \n {\n\
+ if ( $debug_lock)\n {\n my $g=new FileH\
+andle;\n open ($g, \">>$fname\");\n print $g\
+ \"\\nDestroyed by $$\\n\";\n close ($g);\n \
+safe_system (\"mv $fname $fname.old\");\n }\n \
+ else\n {\n unlink ($fname);\n }\n }\n \
+ return \"\";\n }\n \nsub file2string\n {\n my \
+$file=@_[0];\n my $f=new FileHandle;\n my $r;\\
+n open ($f, \"$file\");\n while (<$f>){$r.=$_;\
+}\n close ($f);\n return $r;\n }\nsub string2f\
+ile \n {\n my ($s,$file,$mode)=@_;\n my $\
+f=new FileHandle;\n \n open ($f, \"$mode$fil\
+e\");\n print $f \"$s\";\n close ($f);\n }\
+\n\nBEGIN\n {\n srand;\n \n $SIG{'\
+SIGUP'}='signal_cleanup';\n $SIG{'SIGINT'}='s\
+ignal_cleanup';\n $SIG{'SIGQUIT'}='signal_cle\
+anup';\n $SIG{'SIGILL'}='signal_cleanup';\n \
+ $SIG{'SIGTRAP'}='signal_cleanup';\n $SIG{\
+'SIGABRT'}='signal_cleanup';\n $SIG{'SIGEMT'}\
+='signal_cleanup';\n $SIG{'SIGFPE'}='signal_c\
+leanup';\n \n $SIG{'SIGKILL'}='signal_cl\
+eanup';\n $SIG{'SIGPIPE'}='signal_cleanup';\n\
+ $SIG{'SIGSTOP'}='signal_cleanup';\n $SI\
+G{'SIGTTIN'}='signal_cleanup';\n $SIG{'SIGXFS\
+Z'}='signal_cleanup';\n $SIG{'SIGINFO'}='sign\
+al_cleanup';\n \n $SIG{'SIGBUS'}='signal\
+_cleanup';\n $SIG{'SIGALRM'}='signal_cleanup'\
+;\n $SIG{'SIGTSTP'}='signal_cleanup';\n \
+$SIG{'SIGTTOU'}='signal_cleanup';\n $SIG{'SIG\
+VTALRM'}='signal_cleanup';\n $SIG{'SIGUSR1'}=\
+'signal_cleanup';\n\n\n $SIG{'SIGSEGV'}='sign\
+al_cleanup';\n $SIG{'SIGTERM'}='signal_cleanu\
+p';\n $SIG{'SIGCONT'}='signal_cleanup';\n \
+ $SIG{'SIGIO'}='signal_cleanup';\n $SIG{'SIG\
+PROF'}='signal_cleanup';\n $SIG{'SIGUSR2'}='s\
+ignal_cleanup';\n\n $SIG{'SIGSYS'}='signal_cl\
+eanup';\n $SIG{'SIGURG'}='signal_cleanup';\n \
+ $SIG{'SIGCHLD'}='signal_cleanup';\n $SIG\
+{'SIGXCPU'}='signal_cleanup';\n $SIG{'SIGWINC\
+H'}='signal_cleanup';\n \n $SIG{'INT'}='\
+signal_cleanup';\n $SIG{'TERM'}='signal_clean\
+up';\n $SIG{'KILL'}='signal_cleanup';\n \
+$SIG{'QUIT'}='signal_cleanup';\n \n our \
+$debug_lock=$ENV{\"DEBUG_LOCK\"};\n \n \\
+n \n \n foreach my $a (@ARGV){$CL.=\
+\" $a\";}\n if ( $debug_lock ){print STDERR \\
+"\\n\\n\\n********** START PG: $PROGRAM **********\
+***\\n\";}\n if ( $debug_lock ){print STDERR \
+\"\\n\\n\\n**********(tcg) LOCKDIR: $LOCKDIR $$ **\
+***********\\n\";}\n if ( $debug_lock ){print\
+ STDERR \"\\n --- $$ -- $CL\\n\";}\n \n \
+\n \n \n }\nsub flush_error\n {\n \
+ my $msg=shift;\n return add_error ($EXIT_FAILU\
+RE,$$, $$,getppid(), $msg, $CL);\n }\nsub add_err\
+or \n {\n my $code=shift;\n my $rpid=shift;\
+\n my $pid=shift;\n my $ppid=shift;\n my \
+$type=shift;\n my $com=shift;\n \n $ERROR\
+_DONE=1;\n lock4tc ($rpid, \"LERROR\",\"LSET\",\
+\"$pid -- ERROR: $type\\n\");\n lock4tc ($$, \"\
+LERROR\",\"LSET\", \"$pid -- COM: $com\\n\");\n \
+ lock4tc ($$, \"LERROR\",\"LSET\", \"$pid -- STACK\
+: $ppid -> $pid\\n\");\n \n return $code;\n \
+}\nsub add_warning \n {\n my $rpid=shift;\n \
+ my $pid =shift;\n my $command=shift;\n my $\
+msg=\"$$ -- WARNING: $command\\n\";\n print STD\
+ERR \"$msg\";\n lock4tc ($$, \"LWARNING\", \"LS\
+ET\", $msg);\n }\n\nsub signal_cleanup\n {\n \
+print dtderr \"\\n**** $$ (tcg) was killed\\n\";\n\
+ &cleanup;\n exit ($EXIT_FAILURE);\n }\nsub\
+ clean_dir\n {\n my $dir=@_[0];\n if ( !-d \
+$dir){return ;}\n elsif (!($dir=~/tmp/)){return\
+ ;}#safety check 1\n elsif (($dir=~/\\*/)){retu\
+rn ;}#safety check 2\n else\n {\n `rm -rf \
+$dir`;\n }\n return;\n }\nsub cleanup\n \
+{\n #print stderr \"\\n----tc: $$ Kills $PIDCHI\
+LD\\n\";\n #kill (SIGTERM,$PIDCHILD);\n my $\
+p=getppid();\n $CLEAN_EXIT_STARTED=1;\n \n \
+ \n \n if (&lock4tc($$,\"LERROR\", \"LCHECK\
+\", \"\"))\n {\n my $ppid=getppid();\n if (!$\
+ERROR_DONE) \n {\n &lock4tc($$,\"LERROR\", \\
+"LSET\", \"$$ -- STACK: $p -> $$\\n\");\n &loc\
+k4tc($$,\"LERROR\", \"LSET\", \"$$ -- COM: $CL\\n\\
+");\n }\n }\n my $warning=&lock4tc($$, \\
+"LWARNING\", \"LREAD\", \"\");\n my $error=&loc\
+k4tc($$, \"LERROR\", \"LREAD\", \"\");\n #rele\
+ase error and warning lock if root\n \n if (\
+isrootpid() && ($warning || $error) )\n {\n \\
+n print STDERR \"**************** Summary ********\
+*****\\n$error\\n$warning\\n\";\n\n &lock4tc($$,\"\
+LERROR\",\"RELEASE\",\"\");\n &lock4tc($$,\"LWARNI\
+NG\",\"RELEASE\",\"\");\n } \n \n \n \
+ foreach my $f (@TMPFILE_LIST)\n {\n if (-e $\
+f){unlink ($f);} \n }\n foreach my $d (@TM\
+PDIR_LIST)\n {\n clean_dir ($d);\n }\n \
+ #No More Lock Release\n #&lock4tc($$,\"LLOCK\\
+",\"LRELEASE\",\"\"); #release lock \n\n if ( $\
+debug_lock ){print STDERR \"\\n\\n\\n********** EN\
+D PG: $PROGRAM ($$) *************\\n\";}\n if (\
+ $debug_lock ){print STDERR \"\\n\\n\\n**********(\
+tcg) LOCKDIR: $LOCKDIR $$ *************\\n\";}\n \
+}\nEND \n {\n \n &cleanup();\n }\n \n\ns\
+ub safe_system \n{\n my $com=shift;\n my $ntry=s\
+hift;\n my $ctry=shift;\n my $pid;\n my $status\
+;\n my $ppid=getppid();\n if ($com eq \"\"){retu\
+rn 1;}\n \n \n\n if (($pid = fork ()) < 0){retu\
+rn (-1);}\n if ($pid == 0)\n {\n set_lock\
+($$, \" -SHELL- $com (tcg)\");\n exec ($com);\
+\n }\n else\n {\n lock4tc ($$, \"LLOCK\
+\", \"LSET\", \"$pid\\n\");#update parent\n $\
+PIDCHILD=$pid;\n }\n if ($debug_lock){printf S\
+TDERR \"\\n\\t .... safe_system (fasta_seq2hmm) p\
+: $$ c: $pid COM: $com\\n\";}\n\n waitpid ($pid,W\
+TERMSIG);\n\n shift_lock ($pid,$$, \"LWARNING\",\\
+"LWARNING\", \"LSET\");\n\n if ($? == $EXIT_FAILU\
+RE || lock4tc($pid, \"LERROR\", \"LCHECK\", \"\"))\
+\n {\n if ($ntry && $ctry <$ntry)\n {\n \
+add_warning ($$,$$,\"$com failed [retry: $ctry]\")\
+;\n lock4tc ($pid, \"LRELEASE\", \"LERROR\", \"\\
+");\n return safe_system ($com, $ntry, ++$ctry);\
+\n }\n elsif ($ntry == -1)\n {\n if (!shift\
+_lock ($pid, $$, \"LERROR\", \"LWARNING\", \"LSET\\
+"))\n {\n add_warning ($$,$$,\"$com fail\
+ed\");\n }\n else\n {\n lock4tc ($\
+pid, \"LRELEASE\", \"LERROR\", \"\");\n }\n \
+return $?;}\n else\n {\n if (!shift_lock ($\
+pid,$$, \"LERROR\",\"LERROR\", \"LSET\"))\n {\\
+n myexit(add_error ($EXIT_FAILURE,$$,$pid,ge\
+tppid(), \"UNSPECIFIED system\", $com));\n }\n\
+ }\n }\n return $?;\n}\n\nsub check_configurat\
+ion \n {\n my @l=@_;\n my $v;\n \
+foreach my $p (@l)\n {\n \n if ( $p eq \"EMA\
+IL\")\n { \n if ( !($EMAIL=~/@/))\n {\n\
+ add_warning($$,$$,\"Could Not Use EMAIL\");\n m\
+yexit(add_error ($EXIT_FAILURE,$$,$$,getppid(),\"E\
+MAIL\",\"$CL\"));\n }\n }\n elsif( $p \
+eq \"INTERNET\")\n {\n if ( !&check_inte\
+rnet_connection())\n {\n myexit(add_error ($EX\
+IT_FAILURE,$$,$$,getppid(),\"INTERNET\",\"$CL\"));\
+\n }\n }\n elsif( $p eq \"wget\")\n {\n\
+ if (!&pg_is_installed (\"wget\") && !&pg_is\
+_installed (\"curl\"))\n {\n myexit(add_error \
+($EXIT_FAILURE,$$,$$,getppid(),\"PG_NOT_INSTALLED:\
+wget\",\"$CL\"));\n }\n }\n elsif( !(&pg_is\
+_installed ($p)))\n {\n myexit(add_error\
+ ($EXIT_FAILURE,$$,$$,getppid(),\"PG_NOT_INSTALLED\
+:$p\",\"$CL\"));\n }\n }\n return 1;\n \
+ }\nsub pg_is_installed\n {\n my @ml=@_;\n \
+my $r, $p, $m;\n my $supported=0;\n \n my\
+ $p=shift (@ml);\n if ($p=~/::/)\n {\n if \
+(safe_system (\"perl -M$p -e 1\")==$EXIT_SUCCESS){\
+return 1;}\n else {return 0;}\n }\n else\n\
+ {\n $r=`which $p 2>/dev/null`;\n if ($r eq \\
+"\"){return 0;}\n else {return 1;}\n }\n }\n\
+\n\n\nsub check_internet_connection\n {\n my $\
+internet;\n my $tmp;\n &check_configuration \
+( \"wget\"); \n \n $tmp=&vtmpnam ();\n \n\
+ if (&pg_is_installed (\"wget\")){`wget \
+www.google.com -O$tmp >/dev/null 2>/dev/null`;}\n \
+ elsif (&pg_is_installed (\"curl\")){`curl w\
+ww.google.com -o$tmp >/dev/null 2>/dev/null`;}\n \
+ \n if ( !-e $tmp || -s $tmp < 10){$internet=0\
+;}\n else {$internet=1;}\n if (-e $tmp){unli\
+nk $tmp;}\n\n return $internet;\n }\nsub check\
+_pg_is_installed\n {\n my @ml=@_;\n my $r=&\
+pg_is_installed (@ml);\n if (!$r && $p=~/::/)\n\
+ {\n print STDERR \"\\nYou Must Install the p\
+erl package $p on your system.\\nRUN:\\n\\tsudo pe\
+rl -MCPAN -e 'install $pg'\\n\";\n }\n els\
+if (!$r)\n {\n myexit(flush_error(\"\\nProgra\
+m $p Supported but Not Installed on your system\")\
+);\n }\n else\n {\n return 1;\n \
+}\n }\n\n\n\n","\n\n\n\n\nmy $FMODEL =\"\"; \nmy \
+$TMPDIR = \"/tmp\";\n\n\n\n\nmy $NUCALPH = \"ACGTU\
+NRYMKSWHBVD\";\nmy $PRIMNUCALPH = \"ACGTUN\";\nuse\
+ vars qw($NUCALPH $PRIMNUCALPH $TMPDIR);\n\n\nmy $\
+errmsg;\nuse vars qw($errmsg);\n\n\n\nuse Getopt::\
+Long;\nuse Cwd;\nuse File::Basename;\nuse File::Te\
+mp qw/ tempfile tempdir /;\nuse File::Copy;\nuse F\
+ile::Path;\n\n\n\nsub usage(;$)\n{\n my ($errms\
+g) = @_;\n my $myname = basename($0);\n\n if\
+ ($errmsg) {\n print STDERR \"ERROR: $errms\
+g\\n\";\n }\n\n print STDERR << \"EOF\";\n \
+ \n$myname: align two sequences by means of consa\
+n\\'s sfold\nUsage:\n $myname -i file -o file -d p\
+ath\nOptions:\n -i|--in : pairwise input sequence \
+file\n -o|--out: output alignment\n -d|--directory\
+ containing data\n\nEOF\n}\n\nsub read_stk_aln \n \
+ {\n my $f=$_[0];\n my ($seq, $id);\n \n \
+ my %hseq;\n\n open (STK, \"$f\");\n while\
+ (<STK>)\n {\n if ( /^#/ || /^\\/\\// || /^\\\
+s*$/){;}\n else\n {\n ($id,$seq)=/(\\S+)\\s+\
+(\\S+)/;\n $hseq{$id}{'seq'}.=$seq;\n }\n \
+ }\n close (STK);\n return %hseq;\n }\nsu\
+b read_fasta_seq \n {\n my $f=$_[0];\n my %\
+hseq;\n my (@seq, @com, @name);\n my ($a, $s\
+,$nseq);\n\n open (F, $f);\n while (<F>)\n \
+ {\n $s.=$_;\n }\n close (F);\n\n \n\
+ @name=($s=~/>(.*).*\\n[^>]*/g);\n \n @se\
+q =($s=~/>.*.*\\n([^>]*)/g);\n @com =($s=~/>.*(\
+.*)\\n([^>]*)/g);\n\n \n $nseq=$#name+1;\n \
+ \n for ($a=0; $a<$nseq; $a++)\n {\n my $\
+n=$name[$a];\n $hseq{$n}{name}=$n;\n $hseq{$n}{seq\
+}=$seq[$a];\n $hseq{$n}{com}=$com[$a];\n }\n \
+ return %hseq;\n }\n\n\n\nsub sfold_parseoutput\
+($$)\n{\n my ($frawout, $foutfa) = @_;\n my \
+%haln;\n my ($fstk, $cmd, $id);\n open FOUTF\
+A, \">$foutfa\";\n \n $fstk = $frawout . \".\
+stk\";\n \n # first line of raw out contains\
+ info\n # remaining stuff is stockholm formatte\
+d\n $cmd = \"sed -e '1d' $frawout\";\n syste\
+m(\"$cmd > $fstk\");\n if ($? != 0) {\n \
+$errmsg = \"command failed with exit status $?.\";\
+\n $errmsg .= \"Command was \\\"$cmd\\\"\"\
+;\n return -1;\n }\n\n # this gives a\
+n error message. just ignore it...\n %haln=read\
+_stk_aln ( $fstk);\n foreach $i (keys (%haln))\\
+n {\n my $s;\n $s=$haln{$i}{'seq'};\n $s =~ s\
+/\\./-/g;\n print FOUTFA \">$i\\n$s\\n\";\n }\
+\n close FOUTFA;\n return 0;\n}\n\n\n\n\nsub\
+ sfold_wrapper($$$$)\n{\n \n my ($fs1, $fs2,\
+ $fmodel, $foutfa) = @_;\n \n\n my ($cmd, $f\
+rawout, $ferrlog, $freadme, $ftimelog, $fstk);\n\n\
+ # add basename($fmsqin) (unknown here!)\n \
+$frawout = \"sfold.log\";\n $ferrlog = \"sfold.\
+err\";\n $ftimelog = \"sfold.time\";\n $frea\
+dme = \"sfold.README\";\n $fstk = \"sfold.stk\\
+";\n \n # prepare execution...\n #\n #\
+ ./tmp is essential for dswpalign\n # otherwise\
+ you'll get a segfault\n mkdir \"./tmp\";\n \
+\n $cmd = \"sfold -m $fmodel $fs1 $fs2\";\n \
+open(FREADME,\">$freadme\");\n print FREADME \"\
+$cmd\\n\"; \n close(FREADME);\n\n # and go\n\
+ #\n system(\"/usr/bin/time -p -o $ftimelog \
+$cmd >$frawout 2>$ferrlog\");\n if ($? != 0) {\\
+n $errmsg = \"command failed with exit stat\
+us $?\";\n $errmsg .= \"command was \\\"$cm\
+d\\\". See \" . getcwd . \"\\n\";\n return \
+-1;\n }\n\n return sfold_parseoutput($frawou\
+t, $foutfa);\n}\n\n\n\n\n\n\n\nmy ($help, $fmsqin,\
+ $fmsaout);\nGetOptions(\"help\" => \\$help,\n \
+ \"in=s\" => \\$fmsqin,\n \"out=s\
+\" => \\$fmsaout,\n \"data=s\" => \\$ref_dir);\\
+n\n\n\nif ($help) {\n usage();\n exit(0);\n}\
+\nif (! defined($fmsqin)) {\n usage('missing in\
+put filename');\n exit(1);\n}\nif (! defined($f\
+msaout)) {\n usage('missing output filename');\\
+n exit(1);\n\n}\nif (scalar(@ARGV)) {\n usag\
+e('Unknown remaining args');\n exit(1);\n}\n\n$\
+FMODEL = \"$ref_dir/mix80.mod\";\nif (! -e \"$FMOD\
+EL\") {\n die(\"couldn't find sfold grammar mod\
+el file. Expected $FMODEL\\n\");\n}\n\n\nmy %hseq=\
+read_fasta_seq ($fmsqin);\nmy $id;\n\nforeach $id \
+(keys(%hseq))\n {\n push(@seq_array, $hseq{$id\
+});\n }\n\nif ( scalar(@seq_array) != 2 ) {\n \
+die(\"Need *exactly* two sequences as input (pairw\
+ise alignment!).\")\n}\n\n\n\nmy ($sec, $min, $hou\
+r, $mday, $mon, $year, $wday, $yday, $isdst) = loc\
+altime(time);\nmy $datei = sprintf(\"%4d-%02d-%02d\
+\", $year+1900, $mon+1, $mday);\nmy $templ = basen\
+ame($0) . \".\" . $datei . \".pid-\" . $$ . \".XXX\
+XXX\";\nmy $wd = tempdir ( $templ, DIR => $TMPDIR)\
+;\n\ncopy($fmsqin, \"$wd/\" . basename($fmsqin) . \
+\".org\"); # for reproduction\ncopy($FMODEL, \"$wd\
+\");\nmy $fmodel = basename($FMODEL);\nmy $orgwd =\
+ getcwd;\nchdir $wd;\n\n\n\nmy @sepseqfiles;\nfore\
+ach $id (keys(%hseq)) {\n my ($seq, $orgseq, $f\
+name, $sout);\n $seq=$hseq{$id}{'seq'};\n \n\
+ $fname = basename($fmsqin) . \"_$id.fa\";\n \
+ # replace funnies in file/id name (e.g. \"/\" \" \
+\" etc)\n $fname =~ s,[/ ],_,g;\n open (PF, \
+\">$fname\");\n print (PF \">$id\\n$seq\\n\");\\
+n close (PF);\n\n push(@sepseqfiles, $fname)\
+;\n}\n\nmy ($f1, $f2, $fout);\n$f1 = $sepseqfiles[\
+0];\n$f2 = $sepseqfiles[1];\n$fout = $wd . basenam\
+e($fmsqin) . \".out.fa\";\nif (sfold_wrapper($f1, \
+$f2, $fmodel, \"$fout\") != 0) {\n printf STDER\
+R \"ERROR: See logs in $wd\\n\";\n exit(1);\n} \
+else {\n chdir $orgwd;\n copy($fout, $fmsaou\
+t);\n rmtree($wd);\n exit(0);\n}\n","\nuse En\
+v qw(HOST);\nuse Env qw(HOME);\nuse Env qw(USER);\\
+n\n\n$tmp=clean_cr ($ARGV[0]);\nopen (F, $tmp);\n\\
+nwhile ( <F>)\n {\n my $l=$_;\n if ( $l=~/^\
+# STOCKHOLM/){$stockholm=1;}\n elsif ( $stockho\
+lm && $l=~/^#/)\n {\n $l=~/^#(\\S+)\\s+(\\S+)\
+\\s+(\\S*)/g;\n $l=\"_stockholmhasch_$1\\_stockhol\
+mspace_$2 $3\\n\";\n }\n $file.=$l;\n }\n\
+close (F);\nunlink($tmp);\n$file1=$file;\n\n$file=\
+~s/\\#/_hash_symbol_/g;\n$file=~s/\\@/_arobase_sym\
+bol_/g;\n\n\n$file=~s/\\n[\\.:*\\s]+\\n/\\n\\n/g;\\
+n\n$file=~s/\\n[ \\t\\r\\f]+(\\b)/\\n\\1/g;\n\n\n$\
+file=~s/(\\n\\S+)(\\s+)(\\S)/\\1_blank_\\3/g;\n\n$\
+file=~s/[ ]//g;\n$file=~s/_blank_/ /g;\n\n\n\n$fil\
+e =~s/\\n\\s*\\n/#/g;\n\n$file.=\"#\";\n$file =~s/\
+\\n/@/g;\n\n\n\n\n@blocks=split /\\#/, $file;\nshi\
+ft (@blocks);\n@s=split /\\@/, $blocks[0];\n$nseq=\
+$#s+1;\n\n\n\n$file=join '@', @blocks;\n@lines=spl\
+it /\\@/,$file;\n\n$c=0;\n\nforeach $l (@lines)\n \
+ {\n if (!($l=~/\\S/)){next;}\n elsif ($stoc\
+kholm && ($l=~/^\\/\\// || $l=~/STOCKHOLM/)){next;\
+}#get read of STOCHOLM Terminator\n \n $l=~/(\
+\\S+)\\s+(\\S*)/g;\n $n=$1; $s=$2;\n \n $\
+seq[$c].=$s;\n $name[$c]=$n;\n $c++;\n \n\
+ if ( $c==$nseq){$c=0;}\n \n } \n\nif ( $c!\
+=0)\n {\n print STDERR \"ERROR: $ARGV[0] is N\
+OT an MSA in Clustalw format: make sure there is n\
+o blank line within a block [ERROR]\\n\";\n exit (\
+EXIT_FAILURE);\n }\n\nfor ($a=0; $a< $nseq; $\
+a++)\n {\n $name[$a]=cleanstring ($name[$a]);\\
+n $seq[$a]=cleanstring ($seq[$a]);\n $seq[$a\
+]=breakstring($seq[$a], 60);\n \n $line=\">$\
+name[$a]\\n$seq[$a]\\n\";\n \n print \"$line\
+\";\n }\nexit (EXIT_SUCCESS);\n\nsub cleanstring\\
+n {\n my $s=@_[0];\n $s=~s/_hash_symbol_/\\\
+#/g;\n $s=~s/_arobase_symbol_/\\@/g;\n $s=~s\
+/[ \\t]//g;\n return $s;\n }\nsub breakstring\\
+n {\n my $s=@_[0];\n my $size=@_[1];\n m\
+y @list;\n my $n,$ns, $symbol;\n \n @list\
+=split //,$s;\n $n=0;$ns=\"\";\n foreach $sy\
+mbol (@list)\n {\n if ( $n==$size)\n {\n \
+ $ns.=\"\\n\";\n $n=0;\n }\n $ns.=$symbol;\\
+n $n++;\n }\n return $ns;\n }\n\nsub cl\
+ean_cr\n {\n my $f=@_[0];\n my $file;\n \
+\n $tmp=\"f$.$$\";\n \n \n open (IN, $\
+f);\n open (OUT, \">$tmp\");\n \n while (\
+ <IN>)\n {\n $file=$_;\n $file=~s/\\r\\n/\\n/\
+g;\n $file=~s/\\n\\r/\\n/g;\n $file=~s/\\r\\r/\\n/\
+g;\n $file=~s/\\r/\\n/g;\n print OUT \"$file\";\n \
+ }\n \n close (IN);\n close (OUT);\n \
+ return $tmp;\n }\n","use Env qw(HOST);\nuse En\
+v qw(HOME);\nuse Env qw(USER);\n\n\n$query_start=-\
+1;\n$query_end=-1;\n\nwhile (<>)\n {\n if ( /\\
+\/\\//){$in_aln=1;}\n elsif ( $in_aln && /(\\S+\
+)\\s+(.*)/)\n {\n\n\n $name=$1;\n \n\n $seq=$\
+2;\n $seq=~s/\\s//g;\n $seq=~s/\\~/\\-/g;\n\
+ $seq=~s/\\./\\-/g;\n if ( $list{$n}{'name'} && $l\
+ist{$n}{'name'} ne $name)\n {\n print \"$lis\
+t{$n}{'name'} Vs $name\";\n \n exit (EXIT_\
+FAILURE);\n }\n else\n {\n $list{$n}{'name\
+'}= $name;\n }\n\n $list{$n}{'seq'}=$list{$n}{'s\
+eq'}.$seq;\n \n $nseq=++$n;\n \n }\n else\\
+n {$n=0;}\n }\n\n\nfor ($a=0; $a<$nseq; $a++\
+)\n {\n print \">$list{$a}{'name'}\\n$list{$a}\
+{'seq'}\\n\";\n }\n \n","\nuse Env qw(HOST);\
+\nuse Env qw(HOME);\nuse Env qw(USER);\n\n \
+ \n\
+use strict; \
+ \nuse warnings;\nuse diagnostics;\n\nmy $in_\
+hit_list, my $in_aln=0, my(%name_list)=(),my (%lis\
+t)=(),my $n_seq=0; my $test=0;\nmy($j)=0, my $n=0,\
+ my $nom, my $lg_query, my %vu=();\n\nopen (F, \">\
+tmp\");\n\n$/=\"\\n\";\nwhile (<>)\n{\n print F\
+ $_;\n if($_ =~ /Query=\\s*(.+?)\\s/i) { $nom=$\
+1;}\n\n if ( /Sequences producing significant a\
+lignments/){$in_hit_list=1;}\n \n if ($_=~ /\
+^pdb\\|/i) { $_=~ s/pdb\\|//g; }\n if ($_=~ /^(\
+1_\\d+)\\s+\\d+/) { $_=~ s/$1/QUERY/;}\n \n \
+ if ( /^(\\S+).+?\\s+[\\d.]+\\s+([\\de.-]+)\\s+$/\
+ && $in_hit_list) \n {\n my($id)=$1; # \n $id=~\
+ s/\\|/_/g; #\n if ($id =~ /.+_$/) { chop($id) }; \
+#\n $name_list{$n_seq++}=$id;\n $name_list{$n_seq-\
+1}=~ s/.*\\|//g; \n }\n \n if (/query/i\
+) {$in_aln=1;}\n if ( /^(\\S+)\\s+(\\d+)\\s+([a\
+-zA-Z-]+)\\s+(\\d+)/ || /^(\\S+)(\\s+)(\\-+)(\\s+)\
+/ && ($in_aln == 1))\n {\n my $name=$1;\n my $s\
+tart=$2;\n my $seq=$3;\n my $end=$4;\n \n if ($na\
+me =~ /QUERY/i) { $lg_query=length($seq); }\n\n un\
+less ($test > $n) #m\n {\n my(@seqq)= split(''\
+,$seq);\n my($gap_missing)= scalar(@seqq);\n \
+ \n while ($gap_missing != $lg_query) { uns\
+hift (@seqq,\"-\"); $gap_missing= scalar(@seqq); }\
+\n $seq=join('',@seqq); #m\n }\n \n if ($name\
+ =~ /QUERY/i)\n {\n $n=0; %vu=(); $j=0;\n \
+$list{$n}{'real_name'}=\"$nom\";\n } \n else\n {\n\
+ unless (exists $vu{$name}) { ++$j;} \n $l\
+ist{$n}{'real_name'}=$name_list{$j-1};\n }\n \n $\
+list{$n}{'name'}=$name;\n\n $seq=~tr/a-z/A-Z/;\n $\
+list{$n}{'seq'}=$list{$n}{'seq'};\n $list{$n}{'seq\
+'}.=$seq;\n\n $n++;\n $vu{$name}++;\n $test++;\n \
+ } \n \n}\n\nmy @numero=();\n\nfor (my $a=0; $a\
+<$n; $a++) #m\n{\n my $long=length($list{0}{'se\
+q'}); \n my $long1= length($list{$a}{'seq'});\\
+n \n while ($long1 ne $long)\n {\n $list{$a\
+}{'seq'}.=\"-\";\n $long1= length ($list{$a}{'seq'\
+});\n } \n \n push (@numero,\"$list{$a}{'nam\
+e'} $list{$a}{'real_name'}\\n\");\n}\n\nmy %dejavu\
+=();\n\n\nfor (my $i=0; $i<=$#numero; $i++)\n{\n \
+ my $s=\">$list{$i}{'real_name'}\\n$list{$i}{'seq\
+'}\\n\";\n my $k=0;\n \n if (exists $deja\
+vu{$numero[$i]}) {next;}\n else\n { \n for (\
+$j=0; $j<$n ; $j++)\n {\n if (\"$numero[$i]\" \
+eq \"$numero[$j]\" && $j != $i )\n {\n ++$k;\\
+n $s .=\">$list{$j}{'real_name'}\\n$list{$j}{'seq\
+'}\\n\";\n }\n } \n }\n \n if ($k>0) \
+\n {\n my $cons;\n open (SOR,\">tempo_aln2cons\\
+"); print SOR $s; close SOR ;\n open (COM,\"t_cof\
+fee -other_pg seq_reformat -in tempo_aln2cons -act\
+ion +aln2cons +upper |\") ; \n while (<COM>)\\
+n { \n if (/^>/) { $cons =\">$list{$i}{'real_n\
+ame'}\\n\"; next;}\n $_=~ s/\\n//g;\n $con\
+s .=$_;\n }\n close COM; unlink (\"tempo_aln2cons\\
+");\n print $cons,\"\\n\"; print F $cons,\"\\n\";\\
+n } \n else { print $s; print F $s; }\n \
+ \n $dejavu{$numero[$i]}++;\n} #m\n\nexit;\n\n\\
+n\n\n\n\n\n\n\n\n\n","use Env;\n\n\n$tmp_dir=\"\";\
+\n$init_dir=\"\";\n$program=\"tc_generic_method.pl\
+\";\n\n$blast=@ARGV[0];\n\n$name=\"query\";$seq=\"\
+\";\n%p=blast_xml2profile($name,$seq,100, 0, 0, $b\
+last);\n&output_profile (%p);\n\n\nsub output_prof\
+ile\n {\n my (%profile)=(@_);\n my ($a);\n \
+ for ($a=0; $a<$profile{n}; $a++)\n {\n \n \
+print \">$profile{$a}{name} $profile{$a}{comment}\\
+\n$profile{$a}{seq}\\n\";\n }\n return;\n \
+ }\nsub file_contains \n {\n my ($file, $tag, \
+$max)=(@_);\n my ($n);\n $n=0;\n \n if\
+ ( !-e $file && ($file =~/$tag/)) {return 1;}\n \
+ elsif ( !-e $file){return 0;}\n else \n {\
+\n open (FC, \"$file\");\n while ( <FC>)\n {\n \
+ if ( ($_=~/$tag/))\n {\n close (FC);\n \
+return 1;\n }\n elsif ($max && $n>$max)\\
+n {\n close (FC);\n return 0;\n }\n \
+ $n++;\n }\n }\n close (FC);\n ret\
+urn 0;\n }\n \n \nsub file2string\n {\n \
+ my $f=@_[0];\n my $string, $l;\n open (F,\"\
+$f\");\n while (<F>)\n {\n\n $l=$_;\n #cho\
+mp ($l);\n $string.=$l;\n }\n close (F);\n\
+ $string=~s/\\r\\n//g;\n $string=~s/\\n//g;\\
+n return $string;\n }\n\n\n\nsub tag2value \n \
+ {\n \n my $tag=(@_[0]);\n my $word=(@_[1\
+]);\n my $return;\n \n $tag=~/$word=\"([^\
+\"]+)\"/;\n $return=$1;\n return $return;\n \
+ }\n \nsub hit_tag2pdbid\n {\n my $tag=(@\
+_[0]);\n my $pdbid;\n \n $tag=~/id=\"(\
+\\S+)\"/;\n $pdbid=$1;\n $pdbid=~s/_//;\n \
+ return $pdbid;\n }\nsub id2pdbid \n {\n my $\
+id=@_[0];\n \n if ($id =~/pdb/)\n {\n $id\
+=~/pdb(.*)/;\n $id=$1;\n }\n $id=~s/[|¦_]/\
+/g;\n return $id;\n }\nsub set_blast_type \n \
+{\n my $file =@_[0];\n if (&file_contains ($\
+file,\"EBIApplicationResult\",100)){$BLAST_TYPE=\"\
+EBI\";}\n elsif (&file_contains ($file,\"NCBI_B\
+lastOutput\",100)) {$BLAST_TYPE=\"NCBI\";}\n el\
+se\n {\n $BLAST_TYPE=\"\";\n }\n retu\
+rn $BLAST_TYPE;\n }\nsub blast_xml2profile \n {\\
+n my ($name,$seq,$maxid, $minid, $mincov, $file\
+)=(@_);\n my (%p, $a, $string, $n);\n \n\n\n\
+ if ($BLAST_TYPE eq \"EBI\" || &file_contains (\
+$file,\"EBIApplicationResult\",100)){%p=ebi_blast_\
+xml2profile(@_);}\n elsif ($BLAST_TYPE eq \"NCB\
+I\" || &file_contains ($file,\"NCBI_BlastOutput\",\
+100)){%p=ncbi_blast_xml2profile(@_);}\n else \n\
+ {\n print \"************ ERROR: Blast Return\
+ed an unknown XML Format **********************\";\
+\n die;\n }\n for ($a=0; $a<$p{n}; $a++)\n\
+ {\n my $name=$p{$a}{name};\n $p{$name}{seq}=\
+$p{$a}{seq};\n }\n return %p;\n }\nsub nc\
+bi_blast_xml2profile \n {\n my ($name,$seq,$ma\
+xid, $minid, $mincov, $string)=(@_);\n my ($L,$\
+l, $a,$b,$c,$d,$nhits,@identifyerL);\n \n \n\
+ $seq=~s/[^a-zA-Z]//g;\n $L=length ($seq);\n\
+ \n %hit=&xml2tag_list ($string, \"Hit\");\n\
+ \n \n for ($nhits=0,$a=0; $a<$hit{n}; $a\
+++)\n {\n my ($ldb,$id, $identity, $expectati\
+on, $start, $end, $coverage, $r);\n my (%ID,%DE,%H\
+SP);\n \n $ldb=\"\";\n\n %ID=&xml2tag_list ($hit{$\
+a}{body}, \"Hit_id\");\n $identifyer=$ID{0}{body};\
+\n \n %DE=&xml2tag_list ($hit{$a}{body}, \"Hit_def\
+\");\n $definition=$DE{0}{body};\n \n %HSP=&xml2ta\
+g_list ($hit{$a}{body}, \"Hsp\");\n for ($b=0; $b<\
+$HSP{n}; $b++)\n {\n my (%START,%END,%E,%I,%\
+Q,%M);\n\n \n %START=&xml2tag_list ($HSP{$b}{\
+body}, \"Hsp_query-from\");\n %HSTART=&xml2tag\
+_list ($HSP{$b}{body}, \"Hsp_hit-from\");\n \n\
+ %LEN= &xml2tag_list ($HSP{$b}{body}, \"Hsp_a\
+lign-len\");\n %END= &xml2tag_list ($HSP{$b}{\
+body}, \"Hsp_query-to\");\n %HEND= &xml2tag_l\
+ist ($HSP{$b}{body}, \"Hsp_hit-to\");\n %E=&xm\
+l2tag_list ($HSP{$b}{body}, \"Hsp_evalue\");\n\
+ %I=&xml2tag_list ($HSP{$b}{body}, \"Hsp_i\
+dentity\");\n %Q=&xml2tag_list ($HSP{$b}{b\
+ody}, \"Hsp_qseq\");\n %M=&xml2tag_list ($\
+HSP{$b}{body}, \"Hsp_hseq\");\n \n for ($e\
+=0; $e<$Q{n}; $e++)\n\n {\n $qs=$Q{$e}{body\
+};\n $ms=$M{$e}{body};\n if ($seq eq\"\"){$seq=$\
+qs;$L=length($seq);}\n \n $expectation=$E{$e}{bo\
+dy};\n $identity=($LEN{$e}{body}==0)?0:$I{$e}{bod\
+y}/$LEN{$e}{body}*100;\n $start=$START{$e}{body};\
+\n $end=$END{$e}{body};\n $Hstart=$HSTART{$e}{bo\
+dy};\n $Hend=$HEND{$e}{body};\n \n $coverage=(($\
+end-$start)*100)/$L;\n\n \n if ($identity>$maxid \
+|| $identity<$minid || $coverage<$mincov){next;}\n\
+ @lr1=(split (//,$qs));\n @lr2=(split (//,$ms));\
+\n $l=$#lr1+1;\n for ($c=0;$c<$L;$c++){$p[$nhits\
+][$c]=\"-\";}\n for ($d=0,$c=0; $c<$l; $c++)\n \
+ {\n $r=$lr1[$c];\n if ( $r=~/[A-Za-z]/)\
+\n {\n \n $p[$nhits][$d + $start-1]=$lr\
+2[$c];\n $d++;\n }\n }\n $Qseq[$nhits\
+]=$qs;\n $Hseq[$nhits]=$ms;\n $QstartL[$nhits]=$\
+start;\n $HstartL[$nhits]=$Hstart;\n $identityL[\
+$nhits]=$identity;\n $endL[$nhits]=$end;\n $defi\
+nitionL[$nhits]=$definition;\n $identifyerL[$nhit\
+s]=$identifyer;\n $comment[$nhits]=\"$ldb|$identi\
+fyer [Eval=$expectation][id=$identity%][start=$Hst\
+art end=$Hend]\";\n $nhits++;\n }\n }\n \
+ }\n \n $profile{n}=0;\n $profile{$pro\
+file{n}}{name}=$name;\n $profile{$profile{n}}{s\
+eq}=$seq;\n $profile {n}++;\n \n for ($a=\
+0; $a<$nhits; $a++)\n {\n $n=$a+1;\n \n $prof\
+ile{$n}{name}=\"$name\\_$a\";\n $profile{$n}{seq}=\
+\"\";\n $profile{$n}{Qseq}=$Qseq[$a];\n $profile{$\
+n}{Hseq}=$Hseq[$a];\n $profile{$n}{Qstart}=$Qstart\
+L[$a];\n $profile{$n}{Hstart}=$HstartL[$a];\n $pro\
+file{$n}{identity}=$identityL[$a];\n $profile{$n}{\
+definition}=$definitionL[$a];\n $profile{$n}{ident\
+ifyer}=$identifyerL[$a];\n $profile{$n}{comment}=$\
+comment[$a];\n for ($b=0; $b<$L; $b++)\n {\n \
+ if ($p[$a][$b])\n {\n $profile{$n}{seq}.=$\
+p[$a][$b];\n }\n else\n {\n $prof\
+ile{$n}{seq}.=\"-\";\n }\n }\n }\n \
+ \n $profile{n}=$nhits+1;\n return %profile;\
+\n }\nsub ebi_blast_xml2profile \n {\n my ($n\
+ame,$seq,$maxid, $minid, $mincov, $string)=(@_);\n\
+ my ($L,$l, $a,$b,$c,$d,$nhits,@identifyerL,$id\
+entifyer);\n \n\n \n $seq=~s/[^a-zA-Z]//g\
+;\n $L=length ($seq);\n %hit=&xml2tag_list (\
+$string, \"hit\");\n \n for ($nhits=0,$a=0; \
+$a<$hit{n}; $a++)\n {\n my ($ldb,$id, $identi\
+ty, $expectation, $start, $end, $coverage, $r);\n \
+my (%Q,%M,%E,%I);\n \n $ldb=&tag2value ($hit{$a}{o\
+pen}, \"database\");\n $identifyer=&tag2value ($hi\
+t{$a}{open}, \"id\");\n\n $description=&tag2value \
+($hit{$a}{open}, \"description\");\n \n %Q=&xml2ta\
+g_list ($hit{$a}{body}, \"querySeq\");\n %M=&xml2t\
+ag_list ($hit{$a}{body}, \"matchSeq\");\n %E=&xml2\
+tag_list ($hit{$a}{body}, \"expectation\");\n %I=&\
+xml2tag_list ($hit{$a}{body}, \"identity\");\n \n\\
+n for ($b=0; $b<$Q{n}; $b++)\n {\n \n \n\
+ $qs=$Q{$b}{body};\n $ms=$M{$b}{body};\n \
+ if ($seq eq\"\"){$seq=$qs;$L=length($seq);}\n\n\
+ $expectation=$E{$b}{body};\n $identity=$I\
+{$b}{body};\n \n \n $start=&tag2v\
+alue ($Q{$b}{open}, \"start\");\n $end=&tag2va\
+lue ($Q{$b}{open}, \"end\");\n $startM=&tag2va\
+lue ($M{$b}{open}, \"start\");\n $endM=&tag2va\
+lue ($M{$b}{open}, \"end\");\n $coverage=(($en\
+d-$start)*100)/$L;\n \n # print \"$id: ID: \
+$identity COV: $coverage [$start $end]\\n\";\n \
+ \n \n if ($identity>$maxid || $identity<$\
+minid || $coverage<$mincov){next;}\n # print \\
+"KEEP\\n\";\n\n \n @lr1=(split (//,$qs));\\
+n @lr2=(split (//,$ms));\n $l=$#lr1+1;\n \
+ for ($c=0;$c<$L;$c++){$p[$nhits][$c]=\"-\";}\n \
+ for ($d=0,$c=0; $c<$l; $c++)\n {\n $r=$\
+lr1[$c];\n if ( $r=~/[A-Za-z]/)\n {\n \n \
+ $p[$nhits][$d + $start-1]=$lr2[$c];\n $d\
+++;\n }\n }\n \n \n $identifyer\
+L[$nhits]=$identifyer;\n $comment[$nhits]=\"$l\
+db|$identifyer [Eval=$expectation][id=$identity%][\
+start=$startM end=$endM]\";\n $nhits++;\n }\\
+n }\n \n $profile{n}=0;\n $profile{$\
+profile{n}}{name}=$name;\n $profile{$profile{n}\
+}{seq}=$seq;\n $profile {n}++;\n \n for (\
+$a=0; $a<$nhits; $a++)\n {\n $n=$a+1;\n $prof\
+ile{$n}{name}=\"$name\\_$a\";\n $profile{$n}{seq}=\
+\"\";\n $profile{$n}{identifyer}=$identifyerL[$a];\
+\n \n $profile{$n}{comment}=$comment[$a];\n for ($\
+b=0; $b<$L; $b++)\n {\n if ($p[$a][$b])\n \
+ {\n $profile{$n}{seq}.=$p[$a][$b];\n }\\
+n else\n {\n $profile{$n}{seq}.=\"-\";\\
+n }\n }\n }\n $profile{n}=$nhits+1\
+;\n \n return %profile;\n }\n\nsub blast_xm\
+l2hit_list\n {\n my $string=(@_[0]);\n retu\
+rn &xml2tag_list ($string, \"hit\");\n }\nsub xml\
+2tag_list \n {\n my ($string_in,$tag)=@_;\n \
+ my $tag_in, $tag_out;\n my %tag;\n \n i\
+f (-e $string_in)\n {\n $string=&file2string \
+($string_in);\n }\n else\n {\n $strin\
+g=$string_in;\n }\n $tag_in1=\"<$tag \";\n\
+ $tag_in2=\"<$tag>\";\n $tag_out=\"/$tag>\";\
+\n $string=~s/>/>##1/g;\n $string=~s/</##2</\
+g;\n $string=~s/##1/<#/g;\n $string=~s/##2/#\
+>/g;\n @l=($string=~/(\\<[^>]+\\>)/g);\n $ta\
+g{n}=0;\n $in=0;$n=-1;\n \n \n\n foreach $t\
+ (@l)\n {\n\n $t=~s/<#//;\n $t=~s/#>//;\n \n \
+if ( $t=~/$tag_in1/ || $t=~/$tag_in2/)\n {\n \n\
+ $in=1;\n $tag{$tag{n}}{open}=$t;\n $n\
+++;\n \n }\n elsif ($t=~/$tag_out/)\n {\n \
+ \n\n $tag{$tag{n}}{close}=$t;\n $tag{n\
+}++;\n $in=0;\n }\n elsif ($in)\n {\n \\
+n $tag{$tag{n}}{body}.=$t;\n }\n }\n \\
+n return %tag;\n }\n\n\n\n\n","use Env qw(HOST\
+);\nuse Env qw(HOME);\nuse Env qw(USER);\nwhile (<\
+>)\n {\n if ( /^>(\\S+)/)\n {\n if ($list\
+{$1})\n {\n print \">$1_$list{$1}\\n\";\n \
+ $list{$1}++;\n }\n else\n {\n print $_;\\
+n $list{$1}=1;\n }\n }\n else\n \
+ {\n print $_;\n }\n }\n \n","\n\n\nuse\
+ Env qw(HOST);\nuse Env qw(HOME);\nuse Env qw(USER\
+);\n\n\nopen (F,$ARGV[0]);\nwhile ( <>)\n {\n \
+@x=/([^:,;\\)\\(\\s]+):[^:,;\\)\\(]*/g;\n @list\
+=(@list,@x);\n }\n$n=$#list+1;\nforeach $n(@list)\
+{print \">$n\\nsequence\\n\";}\n\n\nclose (F);\n",\
+"\nopen (F, $ARGV[0]);\n\nwhile ( <F>)\n {\n @\
+l=($_=~/(\\S+)/g);\n \n $name=shift @l;\n \
+ \n print STDOUT \"\\n>$name\\n\";\n foreach\
+ $e (@l){$e=($e eq \"0\")?\"O\":\"I\";print \"$e\"\
+;}\n }\nclose (F);\n\n \n \n","use Env\
+ qw(HOST);\nuse Env qw(HOME);\nuse Env qw(USER);\n\
+\n$tmp=\"$ARGV[0].$$\";\nopen (IN, $ARGV[0]);\nope\
+n (OUT, \">$tmp\");\n\nwhile ( <IN>)\n {\n $fi\
+le=$_;\n $file=~s/\\r\\n/\\n/g;\n $file=~s/\\
+\n\\r/\\n/g;\n $file=~s/\\r\\r/\\n/g;\n $fil\
+e=~s/\\r/\\n/g;\n print OUT \"$file\";\n }\ncl\
+ose (IN);\nclose (OUT);\n\nopen (OUT, \">$ARGV[0]\\
+");\nopen (IN, \"$tmp\");\n\nwhile ( <IN>)\n{\n p\
+rint OUT \"$_\";\n}\nclose (IN);\nclose (OUT);\nun\
+link ($tmp);\n\n"};
+/******************************COPYRIGHT NOTICE*******************************/
+/*© Centro de Regulacio Genomica */
+/*and */
+/*Cedric Notredame */
+/*Fri Feb 18 08:27:45 CET 2011 - Revision 596. */
+/*All rights reserved.*/
+/*This file is part of T-COFFEE.*/
+/**/
+/* T-COFFEE is free software; you can redistribute it and/or modify*/
+/* it under the terms of the GNU General Public License as published by*/
+/* the Free Software Foundation; either version 2 of the License, or*/
+/* (at your option) any later version.*/
+/**/
+/* T-COFFEE is distributed in the hope that it will be useful,*/
+/* but WITHOUT ANY WARRANTY; without even the implied warranty of*/
+/* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the*/
+/* GNU General Public License for more details.*/
+/**/
+/* You should have received a copy of the GNU General Public License*/
+/* along with Foobar; if not, write to the Free Software*/
+/* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA*/
+/*............................................... |*/
+/* If you need some more information*/
+/* cedric.notredame@europe.com*/
+/*............................................... |*/
+/**/
+/**/
+/* */
+/******************************COPYRIGHT NOTICE*******************************/
git://source.jalview.org / jabaws.git / blobdiff